Hi striker1211,
Although we do offer some tools to help users delete inactive images, such as the Image Deletion Wizard and the "Exclude images in active listings" filter on the Image Management page, as it sounds like you may already know, our system is unable to tell that an image is being used in an active listing *if* the listing was a result of a relist done directly through eBay.
We do not currently offer any functionality that can rescan your listings and recreate the associations between images and relists done directly through eBay in which they are present, so I'm afraid you will have to do your best to identify those on your own.
As Ed mentioned, we do keep images that have been marked as deleted from your Image Management page on the Deleted Images page within your account for at least 14 days so, if you were to delete an image that is being used in an active listing in error, you should be able to restore it from there.
I'm sorry there is not more we can do for you under the circumstances, but we will take your comments in this regard into consideration when planning future updates to our site. We appreciate the feedback.
-Mike