Hi,
I was looking for a tool that scans all VARs, then scans Saves/Scenes and Saves/Atom/Appearances and delete all duplicates from those directories, leaving everything intact in VARs.
I tried using a tool called VACUUM, but it did a poor job, I had to restore previously backed up VAM folder, because that tool messed up everything. I tried 2 other tools, one was a command line python tool, but they also did little to nothing.
If you are going to test any tool, backup the entire VAM folder to the side.