Claude Desktop: Auto-update loses spaces.json, causing empty project list

Bug: Claude Desktop auto-update deletes spaces.json

Environment

• Product: Claude Desktop (macOS)
• Update path: 1.8555.2 → 1.9255.2 (auto-update on 2026-05-28)
• OS: macOS (Darwin 25.3.0)

What happened

After an auto-update from version 1.8555.2 to 1.9255.2, the Cowork project list in the sidebar was completely empty. All 9 previously configured spaces/projects were gone.

Root cause

The file spaces.json (located in ~/Library/Application Support/Claude/local-agent-mode-sessions/<accountId>/<orgId>/spaces.json) was deleted or not preserved during the update. This file contains all space/project definitions including:

• Project names and folder assignments
• Project instructions (Projektanweisungen)
• Space UUIDs and metadata

Without this file, the app logs [Spaces] Loaded 0 spaces on startup and the project list is empty.

Additional data loss observed

The claude_desktop_config.json was also partially reset during the update:

• mcpServers configuration was removed
• chromeExtension pairing settings lost
• localAgentModeTrustedFolders removed
• keepAwakeEnabled setting removed
• epitaxyPrefs reset to empty arrays

What was NOT affected

• Session files (local_*.json) remained intact
• Space memory directories (spaces/<uuid>/memory/) remained intact
• The spaces/ directory structure was preserved, only spaces.json was lost

Resolution

The spaces.json file was recovered from a Time Machine backup. After restoring it and restarting the app (rolled back to 1.8555.2), all 9 projects reappeared.

Expected behavior

Auto-updates should preserve spaces.json and all user configuration in claude_desktop_config.json.

Suggested fix

• Ensure spaces.json is not deleted during the update process
• Back up user configuration before applying updates
• Validate that critical user data files still exist after update completion