HI Robin,
If there are items in the store window that you are no longer selling, you can make them hidden in your Auctiva store by going to Auctiva -> Store(tab) -> Edit Items . On this page you have the option to make listings hidden. Listings that are hidden will not be displayed in your Auctiva store nor will they be displayed in your Auctiva store window the next time it refreshes...it does so about every 2 hours.
When you have listings removed by eBay, you'll have to do this for them to be removed from the store window quickly.
-Mike