HQ Music for BGT moves all files added by mods from the music folder to .\1pp_hq_music_BGT\convert\backup and leaves over only empty folders in the music folder.
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The files inside the folders above should also get converted!
They definitely should, the problem so far has been that I can't reproduce the situation on my end when they disappear without being converted. For instance, I have a working BWS mega-install with some of the mods from your list (Jarl's BGT Adventure Pack, RoT, Amber), and with 1PP_HQ_MUSIC_BGT installed finely on top. All the music files were converted and returned to their respective subfolders within the music folder during installation. Unfortunately, I can't begin fixing the problem until I understand what goes wrong. By the sound of it, I'm guessing either the converter crashes sometime after it moves each ACM file for processing and before moving the new file back, or it fails to move the file back (permissions problem?).
I'll do more research on this the next time I get a free weekend, but for now consider me puzzled with why this might be happening; sorry for the trouble.