I realize you were just experimenting, pmonk. But if you need it here you go:
Shntool can output the fixed files in any audio format recognized by shntool, which includes shn, flac, wav and several others. Just insert the '-o [format]' argument after the fix argument, e.g.:
shntool fix -o flac *.flac
If you run a fix like this, only the files that need fixing will end up fixed. You will recognize them by '-fixed' being appended to the name. You can then delete their corresponding unfixed versions and you will end up with a fixed set consisting of a mix of unfixed and '-fixed' files (unless all of them had to be fixed).
Use the -noskip argument if you are outputting to a format
different from the input format. This way shntool will convert those files which it doesn't actually need to fix, e.g.
shntool fix -noskip -o flac *.shn
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