None that I'm aware of, and I've done a lot of tracks using the curent version. I've converted .shn and .wav to .flac with perfect results. The versions we refer to are scthom's encoder. The FLAC algorithm itself has versions, too, but they are more or less in sync, AFAIK.
If you are going from APE to FLAC, try it on one or two files first. Examine them for bitrate, duration, etc, and play them all the way through. Both codecs are lossless, although the tagging structures are different, I'm told. This MIGHT mean some more obscure tag info is tossed, I don't know. I'm just learning this myself, but my understanding is that the FLAC tag set is written in stone and never going to change or expand (for the sake of stability and speed), versus APE, which is may see significant expansion in the future, maybe.
So have a look see. The benefit of FLAC is its simplicity and open source development. Flac playback is a lighter CPU burden, by design. Its compression is not quite as small as APE, however.