Can you send me your project?
I'd be happy to take a look.
Usually, if you remove the PA plug-in
from the AE plug-ins folder (temporarily -- put
it in a safe place), and reopen the project,
AE will ignore those effects, giving you the
opportunity to delete them from your Comps.
This requires you to recreate your PA scenes,
but at least the rest of your projects remain intact.