[Five]

WAVE Shows properties of the WAVE data. An 'h' in the first slot
indicates that the WAVE [h]eader is not canonical. An 'e' in
the second slot indicates that the WAVE file contains [e]xtra
RIFF chunks.

http://www.etree.org/shnutils/shntool/doc/README.txt

this means there's something which is not audio included with the WAV file (99% probably: USELESS!). If/when these files are ever converted to FLAC this non-audio data will be stripped off permanently & automatically. There's a way to get SHNtool remove this as well.

Once this data is gone, the wholefile .md5 for the SHN set will never again work for Led Zeppelin 4-9-70 d1t05.shn and Led Zeppelin 4-9-70 d2t01.shn

This is why the SHNtool md5 (.st5) is better, because it ignores any data which is not audio and also generates the same fingerprint for any format.

IMO you should make a secure conversion to FLAC (audio data bit-verified identical), then fix the SBE using SHNtool (or a SHNtool frontend, it looks like you've got something already installed) then do another len check at the end. Keep a backup of the original files until you're finished & positive everything is okay..