Seems like flac fails if no meta data is found. Try something like:
FOR %%A IN (*.WAV) DO (
flac.exe -V -f --keep-foreign-metadata --replay-gain -8 "%%A"
IF ERRORLEVEL 1 flac.exe -V -f --replay-gain -8 "%%A"
flac.exe -t "%%~dpnA.flac"
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