If you're deleting the files with the rubber they stay on the drive, if you select the file you wish to delete and press Ctrl & backspace (I'm going from memory here for PC) it will ask you if you want to delete the file completely.
Also you should go into the audio pool and purge the files, this way it will tell you which files are currenly being used.
I'd make a backup first before you do any of these things until you get used to it.
An alternative is to ask Mr Vai to come down and lay down your guitar parts for you. That way you'll never need to use the rubber
