Hey there,
I was having a very similar problem with Musicbee saying it had synced all my playlists to my DAP running android, and when I looked in the file explorer, multiple playlists were not there. I have some playlists that are several thousand songs, and a couple of those were not carrying over, and then randomly some of the smaller ones. Also another weird behavior was that the syncing process would slow to a crawl once it got to syncing the actual playlist files themselves once all the music had been copied over.
I changed one setting and suddenly the issue has been fixed so I want to share it. I changed the playlists being synced to the DAP from .m3u files to .m3u8 files, and they suddenly work fine every time and they get moved over almost instantly. Not sure if this might help but I wanted to share since this thread is what started me playing with setting trying to figure out what was going on.