We have a new way of Content Indexing where these same files would become the versions of the file and should help with your licensing. Below is the documentation for the same.
Also, if I understand it right, you are setting the individual users on the every file and when the user leaves, you are going and resetting the user from the file which is causing the backup to happen. If my understanding is right, it is probably better ti have user groups and add or remove the user to the user groups rather than adding the user manualy to each file. In case the user leaves, you could remove the user from the user group itself. Correct me if my understanding is wrong here.