Good morning,
I know this problem since DW version 7.1 that I have in the production environment. Behavior is non-deterministic, sometimes deletes files and sometimes not. An additional problem is when you delete the user's Document Trays tables from the database are removed but the directory on storage remains.
I have a dedicated database for Document Trays and a dedicated storage for Document Trays.
Yours sincerely,
Łukasz Łuczak