[BUG] Claude Sonnet 4.5 Persistent Caching of Project Files After Delete and Re-upload

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?

November 2, 2025 at 12:15 AM Pacific Time (US & Canada) time PDT (GMT-0700)

When a file in a Claude Project knowledge base is deleted, modified, and subsequently re-uploaded (even with a new filename), Claude fails to reference the new content and instead provides responses based on the old, deleted version of the file. This issue is occurring within a project operating in Retrieval Augmented Generation (RAG) mode.

Product/Feature:

• Product: Claude Projects (Pro Plan)
• Feature: Project Knowledge Base File Uploads/Indexing

Observed Behavior

• Claude continues to structure its answers and reference key details from the original, deleted version of the file, despite the new file being present in the Project Knowledge section.

The following comprehensive steps were taken via the Claude web UI and chat interface, and none resolved the persistent caching issue. The core problem remains: Claude is referencing the indexed content of the old, deleted file even when a new file with modified content (or a new name) is uploaded.

Methodology: File Management via UI:

• The old file was located and manually removed/deleted using the Project Knowledge file management UI.
• The modified file was then uploaded again using the Project Knowledge Upload Utility in the web UI.
• Full Removal & Re-upload: This process included deleting the old file, waiting a moment, and then uploading the new version (which failed to update the content Claude referenced).

Methodology: Cache Bypass Attempts (Renaming):

• The locally modified file was renamed (e.g., from File A.txt to File A_V2.txt) to bypass potential file name-based caching/indexing issues.
• When prompted in a new chat, Claude still returned information based on the content of the original File A.txt, confirming the cache is based on content indexing rather than just filename.

Methodology: Chat-based Verification & Context Flushing:

• Explicit Instruction: In a new chat session, Claude was explicitly informed that the file had been updated.
• Content Summary Request: Claude was asked to summarize the contents of the newly uploaded file to verify it was reading the correct version. Observed Failure: Claude returned a summary matching the original file's contents.

Methodology: New Session Testing:

• A brand new chat session within the project was initiated after every file management attempt to ensure no lingering conversation history influenced the retrieval.

Methodology: Final Verification (UI):

• The Project Knowledge file list in the UI was checked to confirm the new file (e.g., File A_V2.txt) was present and listed as successfully uploaded.

What Should Happen?

After deleting the old file and uploading the new, modified file (especially if renamed to avoid caching conflicts):

• Claude should index and reference only the content of the newly uploaded file (File A_V2.txt).
• Claude should structure its answers according to the updated content.

Error Messages/Logs

Steps to Reproduce

1. Create a new Claude Project (or use an existing one that is confirmed to be operating in RAG mode - indicated by the "retrieving" status).
2. Upload a file (e.g., File A.txt) to the project knowledge base (/mnt/project/).
3. Start a chat and confirm Claude can answer questions based on the content of File A.txt.
4. On the local machine, modify the content of File A.txt (e.g., change a specific paragraph or key data point).
5. In the Claude Project knowledge interface:

• Delete/remove the existing File A.txt.
• Re-upload the modified file, either with the same name (File A.txt) or a new, unique name (e.g., File A_V2.txt).
• Start a new chat session within the project

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

4.0

Claude Code Version

2.0.31 (Please note I am using Claude UI from https://claude.ai)

Platform

Other

Operating System

Windows

Terminal/Shell

Other

Additional Information

_No response_