In order for all your iTunes music and playlists to show up in younity you need to make sure you're scanning both the directory where your iTunes catalog is located as well as the directories where your music files are located.

So, if you have changed the scanned directories in younity for desktop and it no longer scans the folder where your music files exist or you have all your music on an external drive and have not told younity to scan that drive, then our mobile app will show iTunes playlists but will not have access to your music files or data. 

The fix is to go to your preferences in younity for desktop and make sure you are scanning the folder that contains all your music.