Why can't I sync my iphone 4S to my itunes?

I recently upgraded to IOS 6.1.3. I then went to my iTunes, and it was empty! No songs, videos, nothing! It was a whole new library. I plugged my iphone in. My account name was still on my iTunes. I managed to get all my songs etc back into the library from the laptop. But I have tried syncing my iphone to it, and it comes up saying "Are you sure you want to remove existing music, movies, TV shows, books and tones from this iphone and sync with this iphones library?" I say yes, and it says my iphone is with another library. Does anybody know why this has happened? Is it because I have updated it to IOS 6.1.3? And can I solve it? Also when I tried logging on to the account today, it came up saying "We could not complete your iTunes store request. An unknown error occurred (-50)". I still have everything on my iphone, but I don't want to sync it yet, in case I lose everything. Hope someone can help.

Added (1). So do I uninstall iTunes from my laptop, and then reinstall it?

This happened to me, it is something about the folders it is trying to read. I reinstalled iTunes deleting all existing folders first and it synced.

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