Dyn. Link, After Effects, showing wrong video, wrong AE comps

I'm using the CS4 production premium, XP Pro, HP dc7600 Convertible, Intel(R) Pent. D CPU 3.4GHz, 3.39 GHz, 3GB RAM.
(yes, I know I need a better machine)
I've done my show without a problem for 6 weeks.
This week I had serious issues.
I'm producing a 10 minute show, shot on a green wall, with 3 separate cameras (3shot and 2 closeups).
I produce the show (with photoshop graphics, jpg images, soundbooth rendered and replaced audio, etc) then I do the AE comps last.
When the movie is rendered, the 3 shot suddenly shows up as a close-up, as black, or as media offline graphic.
I cut up the greenwall clips and then use dyn. link to create mulitple new AE comps.  I do this for all the 3shot clips (note: this is one library clip cut into several smaller pieces), then close the AE project.  Then I repeat this process for the Closeup clips (same deal, one library clip cut into multiple pieces then each is turned into a new AE comp).  The finished show has 10-12 comps that are in two separate AE projects.
When I go into the project to figure out what went wrong, I tried to "edit original" AE comp 29, but AfterEffects opens up and it opens A.) the wrong project b.) the wrong comp (it tries to tell me 34 is 29).
The project was fine before I sent it to the Media Encoder.
Help?
Anthony

Jim,
Thanks for the suggestion.  What I ended up doing was using the AE render que to render each clip, then I replaced the linked comps on the Pr. timeline with the fully rendered clips prior to exporting the finished movie.
Solved the problem, but takes way too long.
Something odd that I noticed, when I use dynamic link from Pr. to AE, the library in AE shows the clips but they have the "unknown file type" icons.  In order to make AE do anything properly, I have to select each clip I import into AE and hit Ctrl + H (to relink the file).
Why would Dynamic link import clips from Pr. but defaultly not establish the correct link?
Watching for the "missing or unknown file type" icon is a real time waster, but at least I can re-establish the link and then proceed.
I'm going to try the old process with this in mind to see if that can be the ultimate issue resolver.
Thanks,
Anthony

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