Should I be using Monkey's GUI to decompress the APE to WAV, then encode to FLAC?

Or will I get the same result by just using the convert in foobar and going straight from APE to FLAC?

The results (which can be verified by MD5 sums (or "fingerprints")) are identical.
Go ahead with foobar2000

Make sure you remember to turn off the DSP and Replaygain from the Diskwriter/Converter preferences if you truly want the results to be the same.

Will do, thanks guys.

There was some discussion recently about the official APE decoder and how it may not report invalid checksums properly. I've used a hex editor on APE files to test foobar, and it's decoder works fine so I would recommend it over anything else just to be safe. I've thought about switching away from APE as well mainly because of this, but since I only use foobar and it is 100% reliable with APE files, I decided to stick the format for now. The encoding speed is fast, decoding speed is alright (kind of slow, but faster than most encoders so I don't see it when transcoding), file size at -c3000 is better than FLAC or Wavpack, and CPU usage during playback is generally 3% or less. If I were to switch, I'd probably pick Wavpack since it's pretty close file size-wise, and is better performance-wise. Sorry, just babbling now heh...