Need some community help

[Aliquippakid]

K so I had like ten things to update in cydia a few weeks ago and did all at once. Then noticed everytime I downloaded from the app store when finished I got the sad iPhone. Everythig else seemed fine so I didn't worry. Well now I had a bunch of other things to update so I tried and it gave a message about removing core functions if I continued. So I tried individually and every app gave the same message. I thought it must be ok so I proceded. Now cydia is gone. So I figure it's best just to update. I'd like to go to 4.1. Right now I'm on 3gs 3.1.3. I have never tried to upgrade to a version that was not current but I have saved my shsh with cydia so could someone give me a Guide on what to do in detail. Do I have to update iTunes first? Does anyone have any idea what even happened. Like I said all apps were updated in bulk and I didn't even look at them so no clue which apps caused this?

Is there anybody out there?