Session resume corrupts JSONL: file-history-snapshot messageId collides with message uuid

[wzxklm]

Bug Description

When resuming a session, Claude Code writes file-history-snapshot entries whose messageId values collide with existing message uuid values in the JSONL file. This causes parentUuid chain traversal to break, making a significant portion of conversation history unreachable after resume.

Evidence

Analyzed the JSONL file of the resumed session with a diagnostic script:

Metric	Value
Total entries	330
messageId/uuid collisions	34
Broken parentUuid refs	0
Entries with uuid	251
Reachable from last entry	190 (75%)
Unreachable (lost)	61 (25%)

Collision pattern

Line 3:   type=user,                    uuid=842f0bfe-2c1e-44c0-8655-74ff68c02903
...
Line 217: type=file-history-snapshot,   messageId=842f0bfe-2c1e-44c0-8655-74ff68c02903  ← COLLISION

Lines 217-228 contain 12 consecutive file-history-snapshot entries, all with messageId values that duplicate earlier message uuid values. These appear to have been written during the resume operation.

Impact

• Subagent summary output disappears — messages that were visible during the live session become unreachable after resume
• 25% of conversation history lost — only 75% of messages are reachable via parentUuid chain traversal from the last entry
• Data corruption at write time — downgrading versions does not fix already-corrupted files (consistent with Conversation history missing on resume (except last message) #24304 findings)

Steps to Reproduce

1. Start a conversation in Claude Code (VS Code extension)
2. Use the Agent tool (subagent) during the conversation — observe the summary output is displayed
3. End the session
4. Resume the session
5. The subagent summary output is missing — both from the UI and from Claude's own context

Root Cause Analysis

The file-history-snapshot entries written during resume reuse the uuid of the original messages as their messageId. When the parentUuid chain is traversed, these collisions create ambiguity — the traversal can jump to a snapshot node instead of the real message node, breaking the chain and orphaning downstream messages.

Environment

• Claude Code running in VS Code extension
• Model: claude-opus-4-6 (1M context)
• Platform: Linux
• Context usage at time of issue: 7% (71.7k / 1000k) — well below compaction threshold

Diagnostic Script

import json

session_file = "path/to/session.jsonl"
entries = []
with open(session_file, 'r') as f:
    for i, line in enumerate(f):
        line = line.strip()
        if not line:
            continue
        entries.append((i + 1, json.loads(line)))

all_uuids = {}
collisions = 0
for line_no, entry in entries:
    uuid = entry.get('uuid')
    if uuid:
        all_uuids[uuid] = line_no

for line_no, entry in entries:
    msg_id = entry.get('messageId')
    uuid = entry.get('uuid')
    if msg_id and msg_id in all_uuids and msg_id != uuid:
        collisions += 1
        print(f"COLLISION at line {line_no}: messageId={msg_id[:16]}... collides with uuid at line {all_uuids[msg_id]}")

# Chain reachability
uuid_to_entry = {e.get('uuid'): e for _, e in entries if e.get('uuid')}
last_uuid = entries[-1][1].get('uuid')
reachable = set()
current = last_uuid
while current and current in uuid_to_entry:
    reachable.add(current)
    current = uuid_to_entry[current].get('parentUuid')

total_with_uuid = len(uuid_to_entry)
print(f"\nCollisions: {collisions}")
print(f"Reachable: {len(reachable)}/{total_with_uuid} ({len(reachable)*100//total_with_uuid}%)")

Related Issues

• Conversation history missing on resume (except last message) #24304 — Conversation history missing on resume (same collision pattern documented)
• Subagent output files lost after context compaction #23821 — Subagent output files lost after context compaction
• [BUG] Subagent Resume Missing All User Prompts #11712 — Subagent resume missing all user prompts

[github-actions]

Found 3 possible duplicate issues:

1. Conversation history missing on resume (except last message) #24304
2. [BUG] Session resume loses 80%+ of conversation — progress entries create parasitic forks in parentUuid chain #35024
3. [BUG] Conversation chain breaks mid-session - earlier messages lost on resume #21617

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🤖 Generated with Claude Code

[github-actions]

This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.