.trash-999

When I used my Linux USB (Xbuntu) to delete the old Windows Protected folders it placed them in a Linux recycle bin (.trash-999) on the same HD partition, who knew. I discovered it when back in windows. I should have emptied recycle before leaving Linux. In my case it was a good thing because I was able to pick up a few files that were not backed up.

I assume booting back into Linux and emptying trash will do the trick. Many of the files still hold their permissions while I am in the Windows system so I can't delete them from Windows.

And the answer is yes. From Linux open the Windows Data folder, then open that folder's trash and delete the files. Now when back in Windows .trash-999 can be deleted if you wish. I am not sure if USB Linux will create it again by simply running or if it only creates if you delete something from within Linux. It doesn't hurt anything being their empty.