Thanks GNAS! I just figured that out and am coming back to post that work around. :)
To delete your protected Bittorrent folder...
1. Turn on your Web Access - Service Setup
2. In Web Access - Folders Setup set Web Access Settings to "Allow All Groups/Users" for folders that have Bittorrent folder in it.
3. Log into your Linkstation via www.BuffaloNAS.com
4. You'll notice that there's a DELETE link next to folders. You should be able to delete the Bittorrent folders via this link.
I've cleaned my drive up by removing 4 of these darn folders. Whew! Of course the question would be through web access, shouldn't the protected folders stay protected??? Hahaha. Thanks for the response GNAS.