selecting the tracks on the iPhone, when it's connected to iTunes, does not do anything to the tracks on the iPhone.
If you create a new playlist, which does not contain any of the tracks that are currently on the iPhone, then at the sync all the current iPhone tracks will be deleted.
The other day I updated my iTunes to the 11.1.5 and have been having issues managing my music on my iPhone since. Here's the problem. I was going to change music on my phone (always manually) so I hook up the phone and computer, select all of the music on the phone, delete and sync. looks good, this how I've been doing it but when I auto fill the new playlist it only does the partial playlist and all of a sudden the old music is still there but not showing up in Itunes only on the phone. I manually delete music via the phone which sucks horribly bad. And there are still grey'd out songs that I can do nothing with. Any ideas whats going on?