After 5.1 update not all apps restored?

i installed 5.1 tonight 4.x. install went fine after 20% of apps reinstalled on phone. seem located in itunes grayed out. there check box in itunes when check it says "all apps on iphone , data replaced apps itunes library?"

worried if yes loose of notes on note pad. develop apps use information use , worried that information gone too!

do?

 

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