[Sosa]

I've had this problem on my iPhone 5 and now it got worse with my iPhone 6s: half or more of my extensive iTunes music library is not synchronizing with my phone. Formerly I would go to the iTunes store on the phone and re-download my purchased songs and everything would be there. When I recently purchased the iPhone 6 I proceeded to do that extra step after synchronizing. As usual only 250 songs were shown in the recently purchased and not on this iPhone menu, which I'm not sure if accurate since I have over 1000 songs purchased. Anyway a full half of my library, if not more, is not on my iPhone and appears greyed out. I do not have an option to redownload and when I try to play I get a message that it isn't available to reproduce, although sometimes it says I need to be connected to WiFi to play.

I am mystified by this. All of those songs are on my iTunes on my iMac. Why are they not being synchronized? I have plenty of space. It is a great variety of music, including gaming soundtracks I took from downloaded games on the Mac, so it is not related to expiring licenses.

[subego]

This may be a silly question, but do you have iTunes (on your Mac) set to sync all your music?

[Sosa]

Yep, silly question! I can't determine a pattern as to what gets copied and what doesn't. Also looking through my song list, I see quite a few songs duplicated. Some are downloaded twice, others have one grayed out and the other downloaded. I'm going to try synchronizing and removing iTunes as an option, see if they all get deleted, then try synchronizing them all again.

[anthology123]

Did you by chance use more than one AppleID to purchase your music from iTunes Store?

[badidea]

For years I defended iTunes as a very good and easy to use application against all those iTunes haters (mainly PC crowd) but recently I started to switch sides...and I think that it started with Apple Music being part of iTunes!
My iTunes library is a lot larger than the space I have available on my phone so I have a playlist called "iPhone" which I sync to the phone with iTunes. I haven't done this for a while and recently wanted to get some new music on the phone...that's when the nightmare started!
First I thought that exchanging the music on the playlist and hitting sync should do the job but I couldn't believe how wrong I was - NO, I first had to turn on that iCloud feature, delete everything that was locally stored with Apple Music (I have an account) and start from scratch.
When syncing was finished and all songs from Apple Music re-loaded, most of my own Music was still greyed out as you describe above...and I had no clue why!
I did this whole process more than once until I eventually had success...after more than 3 hours trial and error...and in the end I had no idea why it finally worked...

[subego]

I've stayed away from Apple Music specifically because it seems capable of leveraging iTunes Match technology to destroy people's music libraries.

Plain iTunes Match is actually pretty awesome.