Is that library part of a Deduplicated Storage Policy by any chance? If so, there's a good chance that some of the deduplciated blocks still exist on that library (or at least, the SP/Dedupe database think they do).
Do you see any associations for that library on its properties? Any Storage Polciies still pointing to it?
I can look into 'hiding' the library if that's the only route available, though we should look into ensuring that the library is truly 'free' in the commCell and that no Polciies think the library is still an option.