In CS5.5., I use the media manager to make a trimmed copy of my project for archiving (I select all the sequences) yet it won't bring along any after effects files (.aep) that were used in the premiere project. The end result is a trimmed copy sans any .aep files, so for now I bring the .aep files in manually but is there a reason/solution to this?
Did you use ADL (Adobe Dynamic Link) to get your AE Comps into PrPro?
is there a solution to this?
Yes. Use the proper tool for the job. For file management, you use a file manager, not an NLE. That means Explorer or Finder.