Ok, that's good. Deleting the products kills the affiliate links as well, but since you are using HOP links, I have a solution for you. In 15 days, we are launching a "common" affiliate program for your whole account. So you provide a URL, a percentage and that's it. So program won't be associated with products individually.
Once this is launched, you can delete the products and the dead affiliate links will automatically repoint to your common URL (as long as they are the "hop" link ones).