As rogerdpack commented, the command line:
ffmpeg -i inputfile.flac output.wav
should do exactly what you want.
Addressing your concerns about keeping the resulting audio intact, FLAC is a lossless format and decoding it to raw PCM stored in a WAV file will keep perfect fidelity. The only thing you might have to be concerned about is if your FLAC file is a higher than normal bit depth like 24, 32 or 64 bits per sample, or has a crazy multichannel configuration. I haven't kept up on whether FFmpeg supports all those combinations. However, most FLAC files are just 16-bit, 44.1 kHz audio files, so this shouldn't be an issue.
About scrubbing metadata, check this Superuser question.