I think you'll have trouble unless you backup and restore the extra bits (system, hidden, archive) as well.I wrote a patch for msdosfs which maps these to suid/sgid/sticky (yes, I know, gross, but it was useful at the time). You can have it if you want.
mtools has a command mattrib which can be used to store FAT attribs, I have used it like so:
mattrib -/ -p c:/'*' > tempfile
tempfile will be a shell script you can execute to recreate the attributes.
/mark
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