Project Manager not working with nested AE Comps

[Margthecar]

I was hoping to trim down the unused media in a rather complicated project. There is one main Sequence, Sequence 01, that has a few dynamically linked AE Comps in it. Sequence 01 also has many nested sequences in it that also have dynamically linked AE Comps in them. The whole project is very big, and I was hoping to use the Project Manager to create a Trimmed project. I read that you have to tell the PM to include all the nested sequences and that you have to relink the AE comps. Okay, I am not opposed to a little manual work, but here is what happens when I try to us PM to create a trimmed project:
In Sequence 01, the AE Comps there are present in the timeline but offline. Once I use Link Media to relink them, they work fine.
BUT in the nested sequences with AE Comps, the video timelines are completely blank, empty, nada, although the audio portion is there. So there is nothing to relink. Not even the original, non-AE video is there.

So, is there a way to get the project manager to recognize and include the AE comps in the nested sequences, as it does for the unnested Sequence 01, even as offline, so I can then relink them?

Alternatively, is there a way to trim clips to only the used portion after that clip has been turned into an AE comp? Then i can at least get my project down in size a bit before I store it, even if I have to do it manually clip by clip. I know which are the big ones I need to trim down, but not sure how to go about it after the project is done.

If what I am trying to do (i.e. trim clips that are part of nested AE comps to only the used portion) is actually impossible, that would be useful to know too. If indeed this is the case, what do you'all recommend to prevent this problem in the future--always pre-edit clips to their shortest length prior to editing?

[momoffduty]

I don't have dynamic link, but was wondering if you highlight all of the sequences you want and then open up the Project Manager?

I use the Collect Files in AE and having problems with 2nd generation projects. In this case too much is collected as if AE is confused.