Hmmmm.....well, the best solution for store-inventory is to avoid the under-stocked/over-sold problem by not relisting until restocked (obviously).
The new Auto-relist and Inventory features on Auctiva are what I'm about to explore as solution.
If you're multi-listing to other venues, you could at least debit inventory to keep track with perhaps a safety margin to prevent over-sold.
***CEO JEFF*** This is why selling/linking with other venues is more than a minor issue. Tracking for that should be at least considered, just as selling from a back-end eComm store (many already have them). To get inventory really working, all sales need to be accurately tracked. Manual debits of inventory are cumbersome at best, and perhaps unworkable for large scale sellers. Just my thoughts.....
You can hide items in the Auctiva store, but I'm not aware of a method on ebay. I wonder if there's a "vacation" option, that temporarily suspends. Seems I recall something like that, but it probably would suspend all items/sales.
Danno
Edit: There is a "vacation" hide feature, but as I suspected, it's all store items. See link:
http://pages.ebay.com/help/specialtysites/placing-store-vacation.html