I've run into the same exact problem, and since January have had to re-upload at least 500 store itmes twice now.
If there is no easy way to allow automated editing, then some automated way of ENDING the auctions would be a godsend. At least then you could mass kill the store items, then use aw2k to mass re-upload them. If you think about it, it's a lot simpler than most of AW2K other automations - Ebay only asks 2 questions - ID#, and Explanation.
BTW...last time I re-uploaded I went with the AW2K supported 120 day auctions. I just didn't have it in me to hand edit every auction AGAIN ;-)