(Thanks for this package; I'm not currently a user, but elpy, which I use, pulls it)
I just typed ffip-diff-apply-hunk by mistake, and the hunk didn't apply. This caused ffip-read-file-name-hijacked-p to not be set to nil, and all subsequent read-file-name calls to use ivy (this was doubly confusing, because I've never use ivy either).
That variable should be reset in all cases; ideally, the advice itself should be removed after the function completes.
Thanks!