Trader's Little Helper will convert SHN > FLAC without decompressing to WAV first. Just drag your SHNs into TLH, select 'convert encoding format', FLAC level 8, then hit convert. Note that if there are any non-canonical headers ('h' in middle column of len check) or extra junk in the the header that these will be automatically stripped when encoding to FLAC. So if your original SHN set contained header errors, then converting to FLAC will change the WAV md5. It would be a good idea to note in the text file what version of FLAC was used (in TLH go to Help menu > About), the len check of the original SHNs, the len check of the FLAC conversion, and how you fixed SBE's if there were any and if you chose to fix them.