The music converter/download tool breaks in wine (and maybe in windows too since the nature of the bug suggests it) if your path has in any way a '-' in it (i think it was the reason).
Results in a dir with a single pcm file named "Edition-.pcm" or something like that.
I didn't fix the bug, just renamed one of my files to 'a.sfc', placed them on my home and worked there, which worked.
Then i used bash wizardry to rename one of the 'set' with:
for f in $(find . -type f); do mv -v "$f" "Final Fantasy VI - T-Edition${f##*/a}"; done
This turned them all into the 'right names' for one of the roms (a.sfc).
Then i moved the patched rom out, made another empty directory - named 'a' in this example -, opened the command line in the directory with all the pcms and did this
(for directly didn't work because the argument kept being divided into spaces when passed to the parameter substitution for some reason - it probably didn't happen above because i had put the files in a path without spaces and named them a.ext - so i'm basically never using a for to process files again if i can help it. I'm sure changing the IFS would work but that would be actual script not a one liner in bash)
find . -type f -exec bash -c 'ln -T "$0" "../a/Final Fantasy VI - T-Edition EX${0##*/Final Fantasy VI - T-Edition}"' "{}" \;
The ln wastes a lot less space than remaking another 3.1 gb of pcm data just for the EX rom, and it's probably something you should look into.
Windows has user side symbolic links support now, that would work almost as well as hardlinks ('almost' because they break when moved, or if you make them relative, break when you don't move both pointer and pointee, and because if you delete the pointee, the symlink is useless, unlike hardlinks).