Thanks for writing in and sorry about the frustrating experience. While you can create several sites with Square online, the items will sync between your stores. When you delete an item from your item library, it will be deleted across the board. Instead of deleting an item, you'll want to edit the item visibility. You're able to make items available across one, or multiple sites this way:
Unfortunately, items can't be "un-deleted", so you would have to recreate any items that are no longer in your library.
