Again not to worry, your Auctiva store is not a duplication of your ebay store, nor does it create a conflict. The Auctiva "store" does not function as a store like ebay's but more like a 'gallery' - it is merely a display of your active listings on ebay. In other words you can not "stock", or directly buy from the Auctiva store, but it is still good way to give your items more exposure. In the future, Auctiva plans to make it a functional store like ebay's. There are many posts on this board that discuss these stores, lots of good info from very knowledgeble Auctiva members.
PS - You are not the first to have a panic attack over this. There must be at least one new attack per day. There needs to be more advance notice to new members. All your items should come back online, just keep checking on them.