If all files on the disk are the same except the last, it recognises them
as the same, because of save data.  This causes problems for at least two
disks, and there may be more.  If there is a difference between what you
have and the disk which was used to make the ingredients.dat file, FDSwin
will indicate which side has a different file, and the CRC of that file.
So you might have Metroid (v1.1) and Metroid (v1.1) [1-c2fbbaaa].  This
means that the last file on side 1 is not what was expected.  For metroid,
this is a save game and does not affect the gameplay or the graphics.  This
file is moved into the ren\ dir.  It may be a dupe, it may not be.

The files that end up in the dupes\ dir are duplicates in the areas which
are important, but might have or miss some additional information which
is found at the beginning of the disk.  I might be able to repair this
information soon, but maybe not.  It will not affect gameplay at all,
since the disk system BIOS does not use it at all.  'Zero Unused Space'
will set these areas to all 00, and also set the bytes after the last
file to all 00.  Also note that some disks have the number of files set
to a certain number, but more files than that are on the disk.  I don't
know which to trust, so it does not remove the 'extra' file.  It might
be garbage, or not.
