Alas, the Touch and Vox are very different.

I'm guessing that the fastest way to clean out that many books is to delete all of the files from the Touch (including the .kobo directory) then re-adding the books. That will ensure the database is clean and the covers are deleted. You will need to reregister, but you won't have to reinstall the updates.

The second fastest way is to switch Calibre to device mode, select the books you want to remove (use ctrl or shift to select more than one at a time), the tell Calibre to remove the books. This will probably be a bit slower since it sounds like you're removing more books than you want to keep. I also don't know if the Touch will automatically clean up the database or if Calibre removes the covers.