Hello
I had the same problem, so I fixed it by taking a blank frame from the AE export and making the entire duration of the piece… lucky it was only a few minutes… and placing that stretched frame across the length of the time line and RENDERING… It fixed the flashing… but anytime I changed anything on the layers below I had to re-render. So i just turned off the top “fix” layer until I was totally done. I presume you could just export a blank document with a similar length of the final FCP file out of AE with the same Alpha info and that would work too, but then when would you get time to check COW. Isn’t that what rendering is for?
Hope this helps.
Andy