New motherboard, Backed Up, But will I be Alright?

So my computor broke recentally but I just fixed my computor. I have backed up my hardrive and all so I still have the files on my IPod Touch 4 but I am unsure if Itunes will recognise me as a new user and delete everything on my IPod that I have at the moment and replace it with everything in my Itunes libuary?
I syned my IPod just before my computor broke if that helps in any way. Will all my game progresses still be there?

yes.  XP w/SP3

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