There's a freeware program called db Poweramp, which I use for all my WAV conversion needs. It's very simple to use and I've never had a single problem with it.
FWIW, I too record at 24/48 (on a dr-100 mk II, no less!) and track it out on Cool Edit Pro or Audacity in that format. Use Trader's Little Helper to create 24/48 FLAC. Then, take the original 24/48 WAV files and run them through db Poweramp, converting them to 16/44.1 WAV files. Voila!
PM me if you have any questions, I'd be happy to help.