Hmm, the problem with that is that I used FFF to download metadata without overwriting the old files.
I did come across a sort of kludgy workaround so for future people:
the first is that if you didn't insert them with Polish Book or Modify ePub, Quality Check can search for books with missing covers (under the somewhat misleading "find non-replaceable covers"). That found a bunch.
Then at least for AO3-downloaded fics they all contain the phrase "Posted originally on the Archive of Our Own at" [then url here]. I couldn't get Quality Check to search for that exact phrase so I ended up using
Agent Ransack (need the trial of the paid version for epub searching, or maybe convert to txt and use another program) and the Drop Search Results plugin to mark all of them.