Kev999, you have to do fix the sfz files separately, but that's pretty easy with grepWin which will recursively replace a text string within a file with another string.
You just tell it to replace all occurences of ".flac" with ".wav"
I made great progress this evening since, after an awful lot of needless mouse clicking (hours), I discovered by accident that fre:ac will on its own descend recursively into sub folders.
So you can convert 2000 flacs to wavs in about 10 seconds.
fre:ac crashed on me a couple of times when I asked it to do over 1500 files at once, then I had to go and find out where it stopped and continue from there, but for more reasonable numbers of files it works fine.
You're better off doing the main subfolders one at a time since some of them are already all wav files and fre:ac will reconvert them and you end up with a bunch of xxx.wav.new files that have then to be deleted.
I just finished the audio files conversions of the "Multisamples" folder under Dimension Pro. I still have to take care of the sfz files.
Oh, and so far I've ended up with both wav and flac files in the same folder. I will be deleting all flac files as a separate step.
For those of you who might consider doing a similar conversion, I strongly suggest you make a copy of the Multisamples directory and work on that. Once it's done you can switch it with the original and maybe keep that somewhere safe. Also copy a piece of the directory tree and practice on that with fre:ac and grepWin (or whatever other tools you use) until you're satisfied with the procedure.
The options for fre:ac are a bit obscure. One especially important one is the "Use input file folder if possible". This must absolutely be checked and then the Output folder" will be ignored.