Found a solution:
If you save your music folder other than the default windows "Music" and save it elsewhere (i.e. like a hard drive) and end up missing your playlists when you update/reinstall MusicBee then follow these steps:
(If you haven't deleted your MusicBee folder (linked to your music), it should still contain your library and playlists (.MBP files), this is good news for the next steps)
--> Before you do anything, make a backup of your MusicBee folder. It should be located in your windows default music folder ("C:\Users\<yourusername>\Music\MusicBee") or the music folder you have set up. Make a backup of it elsewhere, just in case. Also, make a backup of your temporary MusicBee folder that is located in C:\Users\<yourusername>\AppData\Roaming\MusicBee.
--> Delete the folders (not the backups).
--> Reinstall MusicBee. There should be a new MusicBee folder at the default location (in your music folder). Before you launch MusicBee, replace your new /MusicBee folder with the backup folder.
--> Launch MusicBee. The Relink Music File Paths should appear. Insert the default path on the left (i.e.: "C:\Users\<yourusername>\Music\MusicBee") and the correct path on the right (where your music files are, and where your initial MusicBee folder was located before it messed up).
It should do the trick. If not, just repeat these steps until you manage to link your MusicBee folder with your music files.
Remember to backup your library & playlists when you update/reinstall MusicBee!