[Five]

you could generate st5 using shntool/TLH from the wav files and while the formatting is a little different the 32 character hash will match up with FFP/st5 from the resulting flac set unless there were SBEs corrected. st5 also won't be altered by any changes to the header data or even lossless format for that matter.

but what Tubular suggests is secure enough imo, enable verify & check fix SBEs.