You just visually compare the shntool md5 info. Take a look at the shntool md5 for the known good seed, and compare that against the info generated by "shntool md5", or a tool that can generate shntool md5 data, like Audophilia I suppose. That's the only current method I know of.
If the numbers (the checksum) matches for every file then they match. This checksum is the fingerprint for the actual music data inside any sort of lossless container like flac or shn, no matter what the format, seekable, matedata changes to the lossless file, the shntool md5 will remain the same.
dd7c2bc1e7d086cc7bbe5587706d8487 [shntool] ph93-02-03D1T01.flac
So if I ran the same thing on a file of the same thing (same exact WAV file) in SHN it would still match.
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