will firefly not copy those over to the share on the WHS?
Firefly doesn’t copy or move anything anywhere. Firefly only needs read only access to the music files to work.
Sounds like someone has written an extra module and added it to Firefly.
You’ll have to take this problem up with HP.
I’m guessing here but I wonder if this “extra bit” simply ignores certain file types?
What is the file extension of iTunes Plus files?