My Iphone won't sync my CD audio files, after having them on my Iphone for years I updated the other day and they all dissapeared, all that's left is songs bought from Itunes.

I've had an Iphone 4 and I have been listening to hundreds of songs no problem for the past year and a half I've owned it. The other day I decided to sync my Iphone to my laptop to get two songs from a CD. After doing this process and approaching it like I usually would (without causing any problems) I checked my Iphone to see if the two songs had downloaded after the sync. I discovered that my Iphone had lost every audio file that was not bought from the Itunes store leaving me with a sliver of songs to listen to. I immediatly checked my laptop (a Windows device) to see if my music was still there, thankfully it's all on my laptop and the songs play without a problem. So I attempted to sync the songs to my iphone several times, but the CD songs would simply not sync (When syncing your Iphone it consists of 5 steps, the progress bar skips steps 3-4, those are the steps when your music syncs). I'm not an idiot, I checked the small details (checking all albums and songs I wanted and checking the 'entire music library' option) as well I checked the big details (making sure my phone and Itunes were up to date, changing the USB to Iphone wire with another just like it). After a couple of hours of tinkering with different ways to sync I was stumped so I decided to restore my Iphone to factory settings. After doing that and setting up my Iphone newly I still could not download those CD files from Itunes to my Iphone. I called apple support and they recommended that I uninstall Itunes and re-install it. Again no success, all my music is still on my laptop working fine, but I can't seem to sync my CD songs from itunes to my Iphone. If anybody has any info please help. -A college student who needs something to listen to everyday on the hour long bus

Amazing steps you've done so far! The great news is this is very unlikely an issue with your iPhone.
I've run into a similar issue lately as well. I narrowed it down to one song that was causing 30 songs not to sync. I removed the song from the sync list (unchecked it) and all 29 songs were able to sync.
You may be running into a similar issue. This may be a problem with this version of iTunes, an issue with one song or a group of songs; hard to know for sure. It's important to narrow down and isolate the cause. Most imporantly get that music back on there!
The way to narrow down the casue add just a few songs at a time (even 1, just to get that first sync finished). Manually syncing is what you'll need here.
Plug in your iPhone, on the Summary screen (shows a picture of your iPhone, the iOS version, Restore iPhone....; etc). Under the Options area at the bottom choose to Manually Manage Videos and Music then choose Apply in the lower right. The music that's on your iPhone now should be removed from your iPhone now. You're now able to sync music manually.
The link below explains how to drag the songs from the iTunes library on the computer on to your iPhone which will start the sync. Add just one song just to see if you can get 1 of those hundreds of songs on there. If you can, awesome! Keep adding until you find the song or group of songs that are causing this issue.
http://support.apple.com/kb/HT1535
Please let me know how things are going.
Cheers!

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