[BUG] Edit tool silently no-ops on disk while Read returns the edited content (sub-agent worktrees + main session)

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description:
The Edit tool returns success but the change is never written to disk. The Read tool subsequently returns the imagined post-edit content (an in-memory or cached view), but git status / git diff / awk / grep against the file all show the pre-edit content. The discrepancy is silent — no error, no warning.

What Should Happen?

Expected: Edit either persists the change OR errors loudly. Read should reflect on-disk state, not a hypothetical post-edit state.

Actual: Edit silently no-ops; Read returns stale (post-edit-in-memory) content; subsequent Bash commands see the unmodified file.

Frequency: ~8 incidents in one day across multiple sub-agent dispatches (~7 different isolation: "worktree" agents) plus once in the main session. Approx 30-50% hit rate on the first Edit of a session.

Expected: Edit either persists the change OR errors loudly. Read should reflect on-disk state, not a hypothetical post-edit state.

Actual: Edit silently no-ops; Read returns stale (post-edit-in-memory) content; subsequent Bash commands see the unmodified file.

Environment:

• Claude Code CLI 2.1.148
• Model: Opus 4.7 (1M context) — claude-opus-4-7[1m]
• macOS Darwin 25.4.0
• Multiple parallel sub-agents in isolation: "worktree" mode
• Project: Next.js 16 + TypeScript + git worktrees

Notes:

• The cached Read state survives across multiple Read calls in the same session — it's not a transient cache miss.
• The pattern is most prevalent in nested worktrees (sub-agent dispatched from a sub-agent).
• Suspected cause: the Edit tool's persistence layer may not be writing to the actual on-disk file when the agent's cwd is reported as one path but the harness has the file mounted at another (worktree mounting layer).

Error Messages/Logs

Steps to Reproduce

Steps to reproduce:

1. Spawn a sub-agent with Agent({ isolation: "worktree", ... }) (also reproduces in the main session occasionally).
2. Have the agent run Edit({ file_path: "/absolute/path/to/file.ts", old_string: "X", new_string: "Y" }).
3. Tool returns "The file ... has been updated successfully."
4. Have the agent run Read({ file_path: "/absolute/path/to/file.ts" }) — returns content with Y.
5. Have the agent run Bash({ command: "git diff -- /absolute/path/to/file.ts" }) — diff is empty.
6. Have the agent run Bash({ command: "awk 'NR==<line>' /absolute/path/to/file.ts" }) — prints the pre-edit X.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.148

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_