No items were auto-deleted during the downtime. Not even the digamma armor. But that is an easy fix when the time comes, as they can just wipe it from player possession without prejudice.
Anyone who looted got banned, and the GMs seem to be sorting out the items to be deleted as they deal with the petitions from account owners.
I kinda doubt we will see any mass deletion of normal items that have already been traded off and tradeskilled, though. Too many variables as to the circumstances of said trades.