Can’t you, simple question, probably not, momentarily separate the website’s data access from the custom file manager ? If it was possible maybe users could send themselves their informations ; and I don’t think it could bother the unexperienced users : in both cases they would be unable to reach it but I know a relatively big part of your users use FileZilla for example.
This is just a suggestion ; I don’t know at all if it’s possible or even smart but in any case… 
