Ok. If this is XP based, no idea because I do not know a way to tier access with UID and GID in XP, and think making many shortcuts would not do much for you either except cut down on edit overhead when you modify things later as needed.

If this were Linux, the easiest thing would be a large number of links to the htaccess file, one link per folder you want excluded (links can be copy-pasted). Ditto BSD. I would try a few soft links, as then you can delete the link and still keep the file in what I had to test with.

I would do this with links or permissions given your large data tree problem. You can fairly easily have subfolders more restricted to specific user than parent folders in things other than Linux(although the reverse is generally NOT true).

A mix of that might work.

It looks like you are using directories to sort instead of indexing in a DB and using a shallow (logical) storage tree structure.

John Danielson.