Happy to help! Unfortunately, there is no way to avoid the position issue on the BeatBuddy as it does base the MIDI song select on the song’s location, but a neat way to avoid this is by using playlists. Playlists can be made and edited without altering the folder structure and you can have up to 17 of them
You will be limited to not being able to move songs around within the playlist just the same once you set up your MIDI controller, but at least you have some more flexibility to make several setlists using the playlist feature and rearrange your main folders without affecting song select. Also this way you won’t accidentally mess all of it up by adding a new folder above the other existing ones
I highly recommend you use BeatBuddy version 4.1.6, it is not going to change your common experience and it will work correctly with the BBMO and even the BB manager, many bugs were fixed and optimizations made. Playlists work best in this version among other things, the song select for playlists does not work in 3.9.9, I believe.
Read more here:
Please refer to this info for how to open those playlist songs with song select:
Hope this helps!