Hi, I'm having a similar problem since the last update of iTunes. Two days ago I just dragged 2 songs from an external HD onto my iPad inside iTunes. Shortly after that a bunch of playlist were disappearing in front of my eyes on my iPad. Those playlists are still shown under the iPad tree in iTunes, but not on the iPad. At first, all the songs were still there. They could be found in the title list and also could be played directly from the iPad when double clicking on them in the playlist from within iTunes.
I realized that all the playlists that are not shown on the iPad were playlists that have been created in iTunes and then dragged to the iPad. Additionally all playlists that were created directly on the iPad were not shown anymore inside iTunes. So I can see one part of the playlists on the iPad and the other part only inside iTunes.
My iPad had still iOS 7.1.2 on it. I called support yesterday, but without any success. I got kicked twice out of the line and had to deal with a bunch of wrong information in general. So there was no way to expect a result.
As a last hope I updated to iOS 8, which as I almost suspected things got worse. First the update to iOS 8 did not bring the playlists back. I then kept experimented and created new playlists. If I create a playlist on the iPad they won't show up in iTunes. (same was true before the iOS upgrade, but it worked still a few ago). Then I created a playlist on the iPad from iTunes and also dragged a playlist from the music folder onto the iPad. The newly created playlists were showing up on the iPad and also changes to the playlist name were propagated after a while. Then I dragged a song from an iPad playlist inside iTunes onto the newly created playlist. The song showed up inside iTunes, but not on the iPad. I tried to drag more songs from the iTunes music folder and from an external drive into that playlist. None of the songs showed up.
I then created another playlist from within iTunes on the iPad and this time I only dragged songs from the iTunes library or an external drive. Those songs showed up on the iPad! But then a few seconds later the playlists that were just created disappeared again on the iPad. I tried this several times. The playlists always disappeared on the iPad after a few seconds, but they still showed up in iTunes.
At first the dragged over songs were still on the iPad and could be found in the titles view e.g. After a few tries however songs suddenly got deleted, too! It seems that all the songs that were in a playlist that only showed up on iTunes and for which I also tried to drag a song from that playlist to a newly created list got deleted. It was a few hundreds of songs. The playlist and the songs still show up in iTunes, but when I want to play them from within iTunes I get the exclamation mark. The songs also don't show up on the iPad anymore.
I don't use any sync function within iTunes. I always have been copying my music and videos manually onto the iPad. I also don't use iTunes to mange my music. Since I use music for work my music doesn't fit on my notebook and iTunes is not able to handle multiples libraries (like one local and one or more on external drives ). I manage my music with Trakor DJ. This is why I always drag music directly onto my iPad.
It seems there is again another major bug in iTunes. I'm getting so sick of it. For almost a half year I was not able to copy music to my iPad due to the snyc bugs (http://robservatory.com/a-nasty-little-itunesios-bug-may-be-causing-media-sync-i ssues/). Now iTunes deletes playlists and songs by itself. When is Apple finally make iTunes and iPad usable again.
I hope someone at Apple can look into that and provide a hotfix. No, no, no, and again no I don't want to re-set my iPad again. I'm sick of getting this advice from every support rep. It never did any good, but costs me hours of my time. Before I do that again I will buy a Surface and don't worry about iTunes anymore. Apple get your act together! Apparently it is not (only) an iOS problem, since it happened on iOS 7 and iOS 8 to me. iTunes seem to mess up things directly on the iPad.
Marcus