I have seen a similar issue, but only when I delete a file whilst scanner is not running. If scanner is active the delete happens in the server pouch database. When I subsequently start a standard client connecting to the server the client file list is correctly updated.
There is a manual process that sorts the system by deleting then rebuilding the database. The process is described in another thread. See https://casparcgforum.org/t/caspar-clients-library-is-stuck/4632