Hey Steve
I understand your pain. Media Manager is not apple’s best tool… I can’t wait for an update.
I don’t know if you tried these steps but they worked for me. It’s not the fastest workflow but it got me through 40x half-hour multiclip shows. (Although I was using 5.1.4… I didn’t try it with 6.x)
First, copy your final sequence into a new project. (I don’t know why but MM likes it.)
2. then right your sequence and click media manager
3. choose create offline, deselect “delete unused media…” and click ok
4. You’ll have a new project with your sequence and all your master clips, reconnect them all manually.
5. Now you get a sequence without multiclips (that’s what MM doesn’t like)
6. Now you can recapture or delete unused media with media manager
Hope this helps
sorry if I misunderstood your problem… this might help others.
cheers
Olivier