exact Ae version? full numbers
when exactly are you getting this error? what are the steps? how do you mean they work fine in Ae? how do they work fine if you are not able to import them? are you able to import them to premiere (I assume you got it installed).
So it turns out, I did a "Collect Files" then stopped 5 mins in. Somehow, the file was still referring the weird collected files so all I had to do was relink.
To answer above: They were already imported, the error showed up everytime I saved.