Hi Steve,
1) If you have listings that've been deleted on eBay and want to remove them from your Auctiva store and store window, you must make them "hidden" in the Auctiva store. To do this, go to Auctiva -> Store(tab) -> Store -> Edit/Select -> Featured Items. Click the boxes next to the items you'd like hidden and click "Make hidden"
2) The store window is refreshed every 4 hours and closed items removed at next refresh.
-Mike