Library gone after installing 9.1.1, now cant sync apps without deleting

I recently installed iTunes 9.1.1. After the upgrade install was finished and iTunes opened up, my library was gone. I had to re-add all of my massive music collection, which took many many hours, and now when I try to copy songs to my phone (which was previously set up for manually add music) it says I have to delete all content on the phone first! Additionally, when I try to organize my apps or sync them from iTunes, it wants to delete them all on the phone first as well. This is unacceptable, as even though I can reinstall them all from the computer, I will lose all the internally saved data on the apps.

Has anyone else had this problem? And does anyone know how to resolve it? How can I get my old library file working again so iTunes wont think this is a different phone? And how can I sync it again without losing all the internal data from my apps??

I seriously did not do ANYTHING other than install 9.1.1, and then this happened..