I posted the following to a few different threads but maybe it will help in your situation as well. I feel your pain. The past several days I experienced sync issues with the iPad Air, having had to upgrade to the latest iTunes release earlier than I expected due to the need to replace my Mac Pro (the hard drive on my previous Mac Pro became corrupted and due to its age, the Mac Pro had become obsolete, preventing me from being able to upgrade to the latest OS releases these past few years. On the positive side, the Mac Pro lasted nine years and I had been able to at least keep current with the latest iTunes releases in general with little problems up until this last release). After restoring all data from my Time Capsule to the new Mac Pro with OS X Yosemite version 10.10.1, upgrading iPhoto data and rebuilding the iPhoto library (which I had not kept current), I attempted to sync my iPad Air via USB cable and witnessed the iPad disconnecting and reconnecting every other second as if I had a bad USB cable/connection. The cable was fine, but this process rendered me without any playlists, music, and photos on my iPad Air (I had over 100 playlists and nearly 5,000 songs and 4,000 photos). As I was not sure if the issue was with my iPad Air, I reset the iPad Air (selected settings, reset, erase all content and settings) to at least make a fresh start and download from my iCloud backup made the previous day. Rather than repeat many of the same other syncing issues others have already noted [i.e., that I also had] and describe what did not work for my situation, I'll just note the steps that eventually did correct my problem and bring my iPad Air back to its proper state (Perhaps following these steps just coincidentally fixed my problems, but after having spent hours as many others have in trying to resolve the syncing issues, I have not since experienced any issues).
First (after loading iTunes on the Mac Pro of course), I selected iTunes, Preferences, Devices and clicked on [placed the check mark on] "Prevent iPods, iPhones, and iPads from syncing automatically." (As noted in Apple's help documentation, this "Prevents devices from automatically syncing with the iTunes library when a device is connected. To sync a device, click the Sync button when the device is connected)." Selecting this option before connecting the iPad Air via USB cable was important to keep the iPad Air from getting hung up in the automatic sync stage that was preventing me from changing any other iTunes preferences.
Second, I made sure that the iPad Air "iTunes Match" option setting was off (Settings, Music, iTunes Match) prior to performing any sync operation. However, I continue to keep the Mac Pro iTunes Match option "on". I then connected the iPad Air via USB cable to the Mac Pro and once the device was recognized in iTunes, clicked on the rectangular device symbol in the upper left section of the iTunes screen. Within the "Options" [center bottom] section of the screen, I clicked on [placed the check mark on] "Sync only checked songs and videos." This is the only Option I had "checked". Next, within the Settings, Music section (left side of the iTunes screen), I clicked on [placed the check mark on] "Sync Music" and selected "Entire music library" and "Include music videos". I also made sure all of my other settings were selected as I intended for Apps, Movies, Books, Tones, and Photos.
Before initiating the Sync process and to ensure that data was appropriately transferred from my iPad Air to the Mac Pro, (within iTunes) I selected File, Devices, and "Transfer Purchases from iPad Air." Once the transfer was complete, I then clicked on the "Sync" button in the lower right section of the iTunes screen. As none of my nearly 100 playlists, 5,000 songs and 4,000 photos were on the 128 GB iPad Air prior to this sync, it did take longer than usual (maybe one hour). Once the sync icon quit spinning in the iTunes window (upper left section of the screen), I made sure to tap on the Music icon on the iPad Air, select Songs, and go to the bottom of the song list to observe if the status indicator, "Downloading xx of xxxx Songs" was continuing to update. It took about another 10 minutes for this message to disappear at which point it appeared the Sync was finished.
I have since purchased additional music, created playlists, and synced successfully multiple times (at least 10 times) between the Mac Pro and iPad Air, always using the USB cable of course. All of my artwork, songs, playlists, photos, and apps are stored on both devices appropriately and not scrambled. Having spent several hours resolving the iPad Air sync issue, I have been reluctant to attempt a sync between my iPhone 5S and the Mac Pro until I install the latest Time Capsule hardware to backup to should issues arise (i.e., my old Time Capsule is obsolete and can only restore to the Mac Pro now and not backup current data).
