[germain]

TLH will convert from shn to flac without having to go through the wav step. First you need to create an st5 of the shn files. After converting to flac, create another flac st5 or ffp. The flac checksums should perfectly match the shn checksums. You can toss the old shn md5's as they will not match and be of no use to anyone with the flac files.

I would not fix sector boundary errors as this will cause the flac checksums not the match the shn checksums causing your flac files to lose their lineage.