I restored my iPhone to version 2.2 and jailbroke using Quickpwn. Everything went fine.

I then went to look for all my apps on my iPhone (from App Store) which I had installed, they were not there. Double checked that the iPhone synced correctly, etc. No problems. Then I realised, I had Categories installed on my iPhone to sort all my icons into folders on the Springboard. Before I updated to 2.2, I did not remove all the icons from the folders back on to the Springboard.

I have reinstalled Categories and all of the app store and Cydia apps are there, just I can only see them through the Categories application.

I am in the process now of sorting them back into folders on the Springboard.

Just thought I would advise you of my error and my brief moment of panic. If you use Categories, remove all icons back on to the Springboard before you restore/update.