Thanks for the answers and your time! I really appreciate your efforts.
As far as I know from version 1.0.12 libsndfile supports FLAC files, and I guess you are using a newer version so the only thing that has to be done is to compile libsndfile with FLAC support (in order to be able to open FLAC files)? If you link Sonic Visualizer to a libsndfile DLL in the Windows build I can provide a DLL with FLAC input support if needed.
@davidf: It's a good idea to use FLAC as storage, as you have said it's a lossless codec. That's what I do