I use iDealshare VideoGo to convert WAV files to FLAC files.

I like its batch converting WAV to FLAC files and its converting WAV to FLAC with the orinial audio quality.

It also can convert WAV to Apple Lossless ALAC, M4A, OGG, MP3, AIFF, WMA, DTS, etc. or convert FLAC to WAV.

It has both Mac and Windows version.