If there's a way, I haven't found it. And it's not for not looking. You'd think beaking the link would be just as easy as making the link in the first place -- like group and ungroup. Yet there doesn't seem to be any way to dissolve an existing link.
What I've done in the past is go back to square one. That is, delete the AE comps from my PPro project. This usually deletes all the clips, all the edits, and everything associated with those clips. Then I re-import the original clips into PPro, and start over. A royal PITA, but it was the only thing I could find that actually worked. I even made a feature request for this in CS5. I just installed CS6 a couple of days ago and haven't checked to see if this change made it into CS6, but I'm not holding my breath.
Make a feature request. The more that are made, the more likely Adobe is to do it.
Also, restarting my computer "re-initiated" the link. Weird.