itunes software upgrade not syncing music
This clearly isn't how an iTunes upgrade is supposed to go. There are quite different strategies for fixing sync issues depending on whether you have a Mac or a PC, so the best I can offer is to work from the script and perhaps ask another question if you have a problem with a specific step.


iOS: Syncing with iTunes (KB HT1386) 


Also, the problem could be entirely on the iTunes end - so it's a bit of a game to eliminate things one by one. You might take your phone to another computer (now that it's presumably erased) and get a good iCloud backup and test syncing there. This will let you focus on either the iPhone or the computer.