CS6 takes my After Effects clips offline.

Hello,
I'm running a Mac Pro 5,1 with 32 gigs of memory and an Nvidia Quadro 4000. I have a timeline contaning nothing but After Effects compositions that reside in three or four different AE project files. All were imported into AE CS6 from CS5.5 (it's a long-term project).
Here's the problem:
When I open Premiere Pro CS6 it takes a long time to populate the Project Panel and timeline with the AE linked clips. Some clips never populate and are replaced with red or yellow "media offline" placeholders. To speed playback, on the rare occasion I get a linked clip in every section of the timeline I try to render the clips. Some work and score a green bar (though clips with lots of effects take extremely long to render). Several render only partially before returning a "compiling error" message. When this happens, others that were linked and rendered can suddenly go offline. Sometimes the entire timeline becomes red placeholders.
A reboot and reopening of Pr used to fix this, albeit without giving every previously-rendered clip a green "rendered" status. Now the project rarely finds even a majority of the clips. None have been moved or renamed and all open up in After Effects. Going back and selecting a clip to relink it can work occasionally, but on several occasions has also caused neighboring clips to drop offline.
This is really the tip of the iceberg when it comes to my CS6 problems of the past week. If I could just get my timeline up and showing green bars for segments I've already rendered then I would at least feel stuck in place, rather than going backwards.
Can anyone help?
Thanks much,
Gene

Hey,
I do not know if my solution will work for you. I have CS5.5 on MacBook Pro (2.2Ghz i7, 8GB ram, OSX 10.7.4) and I had bunch of clips where I had to stabilize them in AE. I used Dynamic Link for that. I didn't find any solution online.
I work on dual monitors so that's why these screenshots below look weird.
First I did, I opened an AE file, with dynamic links. I had 2 of them (2 projects). [somebody gave a good tip to keep all Dynamic Links in 1 AE project]
Second, I marked all the Dynamic Links which could not be found in PrP. I marked them in the files window.
Then I right click on them and "Link Media" BUT, I DIDN'T DO ANYTHING ELSE. PrP found the files itself. So I clicked "Cancel" in the window which popped up.
I don't know if there has to be that order of doing this. I was doing that first time and this is how I did it. Actually by accident.
ohhh. now I see it was in May... sorry, probably you don't need it any more...

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