FTP delete not atomic / verified / transactional (?)

Is this a file restored two different ways, with RecoveryTool silent and hash error from restore?
Size correct? You could certainly run binary compare (e.g. with cmp or Windows fc /b) for clues.

EDIT:

The destination file is always built block by block (for whatever blocksize the backup is using), so
compare errors likely start and end at block boundaries. First block is offset 0. Last may be short.
Assuming the boundaries end that way, the question is what is where the correct data should be?

Independent restore program
Using recovery tool with missing dlist files
both have Python scripts that could be used (or changed) if other opinions or more analysis helps.

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