Seems to me you would want a mount-time option to the FAT fs code to say
"use FAT#<n>", defaulting to the first if no parm given. If that copy of
the FAT has any problems, fail the mount.
Then you'd want the fsck.fat to have a similar option, saying "use
FAT#<n> for the check" - that way if the FATs are out of sync, you could
do a dry run check on each FAT, and go with the one that seemed to be
better. Perhaps even having the tool allow you to pick and choose if
needed (although this would probably be better as a seperate tool, that
allowed you to view a file given a selected FAT and copy it to a clean
file system.)
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