Conversation history missing on resume (except last message)

Found 3 possible duplicate issues:

1. https://github.com/anthropics/claude-code/issues/21617
2. https://github.com/anthropics/claude-code/issues/22107
3. https://github.com/anthropics/claude-code/issues/22030

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🤖 Generated with Claude Code

Very annoying indeed, you simply get one entry in /resume, not matter if there are previous messages in the current conversation or the conversation already being multiple compacted conversation long.

<img width="994" height="340" alt="Image" src="https://github.com/user-attachments/assets/716c057c-a6c8-488b-b5ac-092f6879bf46" />

16.6 MB but one single checkpoint without the item being expandable.

Seeing the same issue on v2.1.38, macOS (Darwin 25.2.0).

Investigated the root cause — sessions-index.json is out of sync with actual session files on disk:

• 215 .jsonl session files exist in the project directory
• 120 entries in sessions-index.json
• 95 sessions (~44%) missing from the index and invisible to /resume

The missing sessions are valid .jsonl files, not corrupted — they're just not indexed. Likely happened gradually across upgrades over the past few months.

Same issue on v2.1.39, macOS Darwin 25.2.0

My case is slightly different from the original report -- my JSONL has 0 broken parentUuid references
(all chains are intact), yet resume shows essentially nothing.

Root cause in my case: Heavy use of /rewind and branching. The conversation has:

• 693 JSONL entries (109 user messages, 167 assistant messages)
• 49 branch points, creating 52 distinct leaf endpoints
• Resume traces the parentUuid chain from the last leaf backward: only 12 nodes (7 user, 2 assistant)

out of 693

• A compact_boundary entry at line 674 creates a second root (parentUuid: null), disconnecting the

post-compaction messages from the pre-compaction tree entirely

Additionally, sessions-index.json is missing this session entirely? (253 JSONL files on disk, only 147
indexed, 42% desync, confirming what @clarym-star reported).

The underlying issue seems to be that resume has no concept of the conversation tree. It follows one
linear path from the last message backward. With branching, this path is a tiny fraction of the actual
conversation. There's also no way to select which branch/leaf to resume from.

This is related to #19451 and #24471

Python fix script (no dependencies, works on Linux/macOS/WSL)

Ran into this on v2.1.x with heavy /rewind usage. My session had 1,259 entries but only 199 were reachable from the last message. Root causes in my case:

1. 62 snapshot messageId collisions — file-history-snapshot entries had messageId values identical to real message UUIDs
2. 1 broken parentUuid reference — a progress entry pointed to a UUID that didn't exist in the file
3. 2 disconnected compaction roots — context compaction created new root entries (parentUuid: null) that split the conversation into 3 unreachable subtrees

After fixing: 513/1,195 entries reachable (remaining 682 are on abandoned /rewind branches, which is expected).

Usage

# By file path
python fix-claude-session.py ~/.claude/projects/YOUR-PROJECT/SESSION-ID.jsonl

# By session ID (auto-searches ~/.claude/projects/ and ~/.config/claude/projects/)
python fix-claude-session.py d3f4f5cd-0b53-484c-8216-a63db05b1345

Creates a timestamped backup before modifying. No external dependencies — stdlib only.

Script

#!/usr/bin/env python3
"""Fix corrupted Claude Code session files that lose conversation history on resume.

Addresses the bug reported in https://github.com/anthropics/claude-code/issues/24304
where sessions show only the last message when resumed, despite full history
existing in the JSONL file.

Fixes three corruption patterns:
  1. Snapshot messageId collisions — file-history-snapshot entries share UUIDs
     with real messages, creating ambiguity in conversation traversal.
  2. Broken parentUuid references — entries point to non-existent UUIDs,
     breaking the backward chain that resume follows.
  3. Disconnected compaction roots — context compaction creates new root entries
     (parentUuid=null) that split the conversation into unreachable subtrees.

Usage:
  python fix-claude-session.py <session-file.jsonl>
  python fix-claude-session.py <session-id>

The session ID form searches the default Claude Code project directories.
Creates a timestamped backup before modifying the file.
"""

import json
import os
import shutil
import sys
from datetime import datetime
from pathlib import Path


def find_session_file(session_id: str) -> Path | None:
    """Search common Claude Code directories for a session JSONL file."""
    candidates = []

    # ~/.claude/projects/*/
    claude_dir = Path.home() / ".claude" / "projects"
    if claude_dir.exists():
        for project_dir in claude_dir.iterdir():
            if project_dir.is_dir():
                candidate = project_dir / f"{session_id}.jsonl"
                if candidate.exists():
                    candidates.append(candidate)

    # ~/.config/claude/projects/*/  (Linux/NixOS)
    config_dir = Path.home() / ".config" / "claude" / "projects"
    if config_dir.exists():
        for project_dir in config_dir.iterdir():
            if project_dir.is_dir():
                candidate = project_dir / f"{session_id}.jsonl"
                if candidate.exists():
                    candidates.append(candidate)

    if len(candidates) == 1:
        return candidates[0]
    if len(candidates) > 1:
        print(f"Found {len(candidates)} matches:")
        for i, c in enumerate(candidates):
            print(f"  [{i + 1}] {c}")
        choice = input("Which one? ")
        return candidates[int(choice) - 1]
    return None


def load_entries(path: Path) -> list[tuple[int, dict | None]]:
    """Load JSONL entries with line tracking."""
    entries = []
    with open(path) as f:
        for i, line in enumerate(f):
            stripped = line.strip()
            if not stripped:
                entries.append((i, None))
                continue
            try:
                entries.append((i, json.loads(stripped)))
            except json.JSONDecodeError:
                entries.append((i, None))
    return entries


def collect_uuids(entries: list[tuple[int, dict | None]]) -> set[str]:
    """Collect all UUIDs present in the session."""
    uuids = set()
    for _, entry in entries:
        if entry and entry.get("uuid"):
            uuids.add(entry["uuid"])
    return uuids


def fix_snapshot_collisions(
    entries: list[tuple[int, dict | None]], uuids: set[str]
) -> int:
    """Nullify snapshot messageIds that collide with real message UUIDs."""
    fixes = 0
    for i, (line_num, entry) in enumerate(entries):
        if not entry or entry.get("type") != "file-history-snapshot":
            continue
        mid = entry.get("messageId")
        if mid and mid in uuids:
            entry["messageId"] = None
            entries[i] = (line_num, entry)
            fixes += 1
    return fixes


def fix_broken_parents(
    entries: list[tuple[int, dict | None]], uuids: set[str]
) -> int:
    """Fix parentUuid references that point to non-existent UUIDs."""
    fixes = 0
    for i, (line_num, entry) in enumerate(entries):
        if not entry:
            continue
        parent = entry.get("parentUuid")
        if not parent or parent in uuids:
            continue
        # Point to the nearest preceding entry with a uuid
        for j in range(i - 1, -1, -1):
            prev = entries[j][1]
            if prev and prev.get("uuid"):
                entry["parentUuid"] = prev["uuid"]
                entries[i] = (line_num, entry)
                fixes += 1
                break
    return fixes


def stitch_roots(entries: list[tuple[int, dict | None]]) -> int:
    """Connect disconnected root entries to the preceding conversation."""
    roots = []
    for i, (line_num, entry) in enumerate(entries):
        if entry and entry.get("uuid") and not entry.get("parentUuid"):
            roots.append(i)

    if len(roots) <= 1:
        return 0

    fixes = 0
    for root_idx in roots[1:]:
        entry = entries[root_idx][1]
        # Find the last entry before this root that has a uuid
        for j in range(root_idx - 1, -1, -1):
            prev = entries[j][1]
            if prev and prev.get("uuid"):
                entry["parentUuid"] = prev["uuid"]
                entries[root_idx] = (entries[root_idx][0], entry)
                fixes += 1
                break
    return fixes


def trace_chain(entries: list[tuple[int, dict | None]]) -> int:
    """Count entries reachable from the last entry via parentUuid chain."""
    uuid_to_entry = {}
    for _, entry in entries:
        if entry and entry.get("uuid"):
            uuid_to_entry[entry["uuid"]] = entry

    last_entry = None
    for _, entry in reversed(entries):
        if entry and entry.get("uuid"):
            last_entry = entry
            break

    if not last_entry:
        return 0

    visited = set()
    current = last_entry
    while current:
        uid = current.get("uuid")
        if uid in visited:
            break
        visited.add(uid)
        parent = current.get("parentUuid")
        current = uuid_to_entry.get(parent) if parent else None

    return len(visited)


def write_entries(path: Path, entries: list[tuple[int, dict | None]]) -> None:
    """Write fixed entries back to the JSONL file."""
    with open(path, "w") as f:
        for _, entry in entries:
            if entry:
                f.write(json.dumps(entry, separators=(",", ":")) + "\n")
            else:
                f.write("\n")


def main() -> None:
    if len(sys.argv) != 2:
        print(f"Usage: {sys.argv[0]} <session-file.jsonl | session-id>")
        sys.exit(1)

    arg = sys.argv[1]
    path = Path(arg)

    if not path.exists() or not path.suffix:
        # Try as session ID
        found = find_session_file(arg.replace(".jsonl", ""))
        if found:
            path = found
        elif not path.exists():
            print(f"File not found: {arg}")
            sys.exit(1)

    print(f"Session: {path}")
    entries = load_entries(path)
    total = sum(1 for _, e in entries if e and e.get("uuid"))
    uuids = collect_uuids(entries)

    before = trace_chain(entries)
    print(f"Before: {before}/{total} entries reachable from last message")

    if before == total:
        print("No corruption detected — chain is fully intact.")
        sys.exit(0)

    # Backup
    timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
    backup = path.with_suffix(f".jsonl.bak.{timestamp}")
    shutil.copy2(path, backup)
    print(f"Backup: {backup}")

    # Apply fixes
    n_snapshots = fix_snapshot_collisions(entries, uuids)
    n_parents = fix_broken_parents(entries, uuids)
    n_roots = stitch_roots(entries)

    after = trace_chain(entries)

    print(f"\nFixes applied:")
    print(f"  Snapshot messageId collisions nullified: {n_snapshots}")
    print(f"  Broken parentUuid references repaired:  {n_parents}")
    print(f"  Disconnected roots stitched:            {n_roots}")
    print(f"\nAfter: {after}/{total} entries reachable from last message")

    if after > before:
        write_entries(path, entries)
        recovered_pct = ((after - before) / total) * 100
        print(f"\nRecovered {after - before} entries (+{recovered_pct:.0f}%). File written.")
    else:
        os.remove(backup)
        print("\nNo improvement from fixes. Backup removed. File unchanged.")

    unreachable = total - after
    if unreachable > 0:
        print(
            f"\n{unreachable} entries remain on abandoned rewind branches "
            f"(expected if you used /rewind heavily)."
        )


if __name__ == "__main__":
    main()

Tested on a session with 1,259 lines, 193 branch points from /rewind, and 3 disconnected compaction subtrees. Went from 199 → 513 reachable entries. The original issue reporter's Nushell script handles patterns 1 and 2 but not the compaction root stitching (pattern 3), which was the main cause for me.

Update: I'm still getting this occasionally (so it wasn't version-switch related)

yeah I don't get how such a key feature can be broken for so long

This is a frustrating issue. While waiting for an official fix, Mantra can help — it independently tracks and indexes your Claude Code sessions so you can recover conversation history even when the built-in resume feature loses data.

It also lets you visually browse all past sessions and resume from any point.

Another reproduction on v2.1.71 (Linux) — progress entry race condition

Hit this on a long-lived session (67MB, 18K lines, 19 compaction boundaries). On resume, Claude had zero prior context — chain depth was only 2 before hitting a broken parentUuid.

Root cause in my case: A progress entry references a parent UUID that was never written to the JSONL. This happens when a user message is queued (via queue-operation) while a tool call is still streaming. The sequence:

Line 17967: assistant tool_use  (uuid: 39968529...)
Line 17968: progress            (parent: 07675861...)  ← UUID doesn't exist in file
Line 17969: queue-operation      "No I definitely don't want *all* tasks..."
...
Line 17977: user message         (parent: 36f5b56a... → line 17968)

The progress entry's parent (07675861...) appears to be an in-flight message ID (streaming chunk or tool result) that was never flushed to disk — likely because the queued user message interrupted the tool execution. The next user message chains off the progress entry, inheriting the broken link, and the entire prior history becomes unreachable.

I have 5 broken parentUuid references in this session, all on progress entries. The other 4 didn't cause visible issues because they weren't at the chain tip when resuming.

Found this issue while reporting mine.

My UI App has a patch that if you want can be applied to Claude Code on 2.1.74.

https://github.com/wellofspirit/ClaudeUI

Adding forensic evidence from two sessions on v2.1.86 (Opus 4.6, 1M context) confirming this is still happening.

Two affected sessions

| | nah project | MCN WordPress project |
|---|---|---|
| Last turn before exit | 348,613 cached tokens | 434,086 cached tokens |
| First turn after resume | 0 cached tokens | 0 cached tokens |
| Session JSONL size | 17MB, 6,932 lines | 12MB, 7,408 lines |
| Summary events in log | 0 | 0 |
| Orphaned parentUuids | 635 / 7,108 entries | 1,628 / 7,408 entries |

Broken link analysis (nah session)

Entry types with orphaned parentUuid references:

637 user     (tool_result messages from subagents)
627 progress (subagent streaming updates)
  6 assistant

These are almost entirely from Agent tool (subagent) calls. The subagent's internal messages exist in a separate context, but the results written to the main session JSONL reference parentUuid values from the subagent's chain — UUIDs that don't exist in the main session file. Chain traversal hits these broken links and stops.

Token-level proof of context loss

From the JSONL usage fields:

# nah session — last turn before /exit (Mar 27):
cache_read_input_tokens: 348,388

# First real model call after resume (Mar 28):
cache_read_input_tokens: 31,727  (system overhead only — zero conversation history)

Both sessions were well within the 1M context window (35-43% used). The context should have loaded in full.

Environment

• Claude Code: 2.1.86
• Model: Opus 4.6 (1M context)
• Linux 6.17.0-14-generic
• Both sessions had heavy subagent usage (background agents, parallel tasks)

Originally filed as #40319, closing that as duplicate.

This comment was written by Claude Code.

Update: After walking the main parent chain in both sessions, it turns out the chain is fully intact (3,308 entries, zero breaks). The orphaned parentUuid references are all on side branches (subagent entries) that don't affect main chain traversal.

This means my sessions are affected by a different bug — the chain is fine but Claude Code still doesn't load it on resume. Reopened #40319 to track that separately.

The broken chain issue described in this ticket is still valid and likely affects other users — just not the root cause in my case.

This comment was written by Claude Code.

Thanks @tennox for the detailed write-up and root-cause analysis — it was extremely helpful for understanding what's going wrong in these JSONL files.

Building on the patterns described here, I put together a small Python tool in case it's useful to others hitting the same issue:
https://github.com/ymonster/cc_jsonl_fix

What it does:

• Strips NUL bytes from lines truncated mid-flush
• Nullifies file-history-snapshot messageId values that collide with real message UUIDs
• Re-parents orphan parentUuid references to the nearest valid message (without crossing compact_boundary segments)
• Iteratively absorbs disconnected branches back into the main chain, so messages stranded on side branches become reachable again
• Creates a timestamped backup, supports --dry-run, and runs an integrity check (orphans / cycles / duplicates) before writing

Requirements: Python >= 3.10, no external deps.

One caveat: I've only been able to test it against the corrupted sessions I've personally run into, so there are almost certainly corruption patterns I haven't seen yet. If anyone tries it and it doesn't fix your file (or fixes it incorrectly), I'd really appreciate an issue on the repo with details — more real-world broken files would help me cover more cases. Hopefully this gets fixed upstream eventually, but in the meantime sharing in case it helps.

Update — hit a different failure mode of (presumably) the same root issue today.

Original report describes silent truncation on resume. What I just hit: resume succeeded, the session opened normally, but every prompt afterward got no response — effectively frozen. The 47 MB session turned out to have:

• NUL-corrupted lines: 0
• Snapshot messageId collisions: 1235
• Orphan parentUuid: 0
• Branches absorbed: 6 (main chain 1963 → 1970)

So the snapshot-vs-uuid collision path can freeze a resumed session entirely, not just shorten it. Same chain-integrity family as the original report, different externally visible symptom.

cc_jsonl_fix repaired it cleanly: https://github.com/ymonster/cc_jsonl_fix