[rkomar]

I guess no one has such a script already. I don't think it needs to be interactive, because it just needs to find data in those directories that doesn't have an existing ebook for it, and then delete it. Thus, you wouldn't need to use the sh_ivtool application for interactivity. I think the script would be a lot simpler if it could use the Unix find utility to look for the .af0 files, since they are spread out in directories that match the structure where the ebooks are. If no one else comes up with such a script first, I'll try to write something over the next few days.

P.S. Deleting books using the Library application usually deletes the extra information, as well. If you are deleting using the USB connection, maybe you should use the Library app instead.