Description

MongoDB's update() method in the vector store used {"$set": {"payload": new_payload}} which replaces the entire payload document on update, causing all existing metadata fields (e.g.,
bucket_id, category, source, context_id) to be silently lost.

The fix uses MongoDB dot notation — {"$set": {"payload.data": ..., "payload.hash": ...}} — which only updates the specified fields and preserves everything else. This is the documented MongoDB
behavior for partial updates on embedded documents.

Fixes #3966

Type of change

• Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

• Unit Test

3 tests added/updated in tests/vector_stores/test_mongodb.py:

• test_update — updated to verify $set uses dot notation (payload.key) instead of full replacement (payload)
• test_update_payload_only_uses_dot_notation — verifies only specified fields appear in $set, no full payload key
• test_update_vector_only_does_not_touch_payload — verifies vector-only updates don't touch any payload fields

All 39 tests pass locally (21 in test_memory.py + 18 in test_mongodb.py).

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings

Maintainer Checklist

• closes MongoDB Implementation Bug: update replaces metadata entirely #3966