Deleted files are shown in Web Interface (after Upgrade OC 8 to 9)

Hello!

We have upgraded our OC server from version 8 to 9.1
One of the user reports that he deletes file , updates page and file is still shown in the Web Interface.
File has been deleted from the filesystem , but still shown in the user web interface.

We upgraded to the latest 9.1.3 and it did not resolve this issue
We ran these commands:
sudo -u www-data php occ files:scan username
sudo -u www-data occ files:cleanup username
the last one returned "0 orphaned file cache entries deleted"

We think that the problem comes from the bad file cache in database (we are running MySQL instance).

Can anyone help with this problem?

Thanks!

Is this on external storage? How does the user delete the file, over web-interface, webdav or oc-client?

Direct modifications to the data-folder are not supported:

The storage is local folder. Folder on the OC server's filesystem.
User deletes file over the web interface

Have you checked you logfiles? Sounds like some database problems.