You’re using FCP 5, right? Media Manager is BROKEN! It almost always screws up your “delete unused media.”
Two options: export and EDL and batch digitize that. or export and XML, import it in FCP 4.5, and use that Media Manager to create an offline project that deletes unused media correctly. I’ve heard all these theories of how to make it work in 5 (making independant clips, etc…) but only the two options above have ever worked reliably.
I’m surpirsed FCP 5 has been out as long as it has and Apple hasn’t addressed this problem. it’s an arsing pain,