[jazzbo]

I think you'll end up having to write a batch file, but another approach to this is to use shntool's md5 command with the -c switch. It will generate a composite md5 of all the files in a directory.

so shntool md5 -c *.shn in one directory should produce the same output as shntool md5 -c *.flac in another directory. To work perfectly, the files would have to be similarly named so the composite output was in the same order, but you'd have that problem with what you're trying to do as well.

I've not used DOS in ages, but there used to be a file compare command (fc), you could redirect the output of both shntool commands into temp files and then compare the results rather easily.

Obviously, if you want to find which file in the shn set is different from the flac set you'll need to do a more precise cmp of each individual file pair.