save() may break database consistency (concurrency issue)

save() only saves changed fields in existing documents, This is pretty fine, but it saves with upsert=True! So, if someone deleted the document in the meanwhile, we end-up with a document with only updated fields (and missing required fields). (We encountered to these mal-structured rows in our database.)

save() should not use upsert=True when updating only changed fields. It may check for results and raise an exception if no document is updated (sqlalchemy has a StaleDataError for this porpose)

Start at save() and trace the existing-document path that updates only changed fields. Verify that a concurrent deletion cannot recreate a partial document through upsert, and that a no-update result produces the intended stale-data exception; add regression coverage for both outcomes.