The problem I had in switching from Apple to GNU/Linux was the "bunch" of
.M4A I have made in iTunes.
If the losless of the m4a format is ok and is playable in VLC, converting
them is another story, because it is not a free format and iTunes didn't
played Flac files (I don't know if it's always the case).
I use avconv (the libre equivalent of FFMpeg) and I do :
$ avconv -i input.m4a output.flac
Convert all tour files can be quite long. Maybe a solution sould exist for
converting cevral files in the same command but I don't know how. FFMpeg
tutorials could tell you to do it.
I don't kow if it's working with WinFF.
Maybe you sould try avconv for your .wmv if everything else has failed.
Remember m4a is a lossless format, not a lossy format ! So convert them in
aiff, wav or flac !
As I said, I don't know why keeping m4a files if it's only really compatible
with iTunes.
iTunes suks !
I also recommand the libre format opus, available in SoundConverter who is
much more better than the old mp3 for a good lossy format for your future
convertions.
https://opus-codec.org/
https://opus-codec.org/comparison/