Clip List incomplete after Save Copy In

[justinhill]

I apologise in advance if I'm being stupid here.... Moving to the next phase of a project, I am using Save Copy In with audio files checked and preserve hierarchy unchecked. The original session has many audio clips which are in an external assets folder.

The new session has everything in its new audio files folder, including the items that were originally external assets, but (obviously) no redundant audio from clips that were no longer being used. The new session looks right and plays right.

BUT... less than half the clips in the session appear in the clip list. For example, there is a music bed called 'Deep Waters' that appears in several places and I am looking at a clip on the timeline called "Deep Waters-01" but there are no clips in the clip list called "Deep Waters". This was previously an external asset - but there are loads of clips not listed which were always local to the session. If I split one of these unlisted clips using Separate, then re-join with Heal Separation, the clip suddenly appears in the list.

What have I done wrong?