I recently jailbroke my iPad 3 and I'll be updating to iOS 6 once it gets released. I am aware that updating the software removes the jailbreak. I want to know what will happen to my jailbroken cydia apps. Will they get erased? How can I back them up with iTunes so that I can restore them after the update (when a Jailbreak for iOS 6 gets released). I read a lot of tutorials on how to sync these kind of apps and a lot of the tutorials say that I should Reset Warnings on iTunes followed by Transfer Purchases but I keep getting that I'm not authorized for the app, but when I click Authorize this computer in iTunes and enter my Apple Store ID, I find that my computer is authorized to my account. iTunes then starts syncing only apps downloaded from the App Store) but Cydia apps don't. The reason I want to sync all my Cydia apps is because as I mentioned earlier I want to update to iOS 6 but I don't want to redownload the apps manually, it will take a lot of time. So if someone can help me I'll be greatly appreciated.
As sn4ke mentioned, your best bet is to buy a Cydia backup tweak such as PKGBackup. You can have the backups stored in Dropbox or in the Contacts app of your iPad. As long as you don't delete the backups while you wait for a jail break for iOS 6, you should be able to download PKGBackup and run a restore after iOS 6 is released and jail broken.
However.
It's always a good rule to download Cydia tweaks manually after a major iOS upgrade (like the jump from iOS 5 to iOS 6). That's because a lot of things get changed in the updates and it's better to re-install tweaks one at a time to make sure you don't develop any conflicts. Usually, a backup program of Cydia tweaks is most effective for minor updates (like iOS 5.0.1 to 5.1.1 was). Yeah, it's a bit of a pain in doing major upgrades, but it sure can save some headaches. Your call, of course - just providing advice.
And - Cydia tweaks are like App Store apps in that, once you've purchased, you own them, you won't be required to buy them again. So, once a tweak has been updated for iOS 6 (and the iPad is re-jailbroken on iOS 6), you can go back and get all your tweaks again.
Why cant I get an answer to this question? I posted the same question yesterday in another iPad forum and I didn't get a reply.
I'll be honest with you and tell you that 6 hours is not enough time to allow for an answer on a forum. This is an international forum and it takes a while for people to see/read your post, let alone respond to it. Our own forum rules require 48 hours to pass before someone should start worrying about not receiving an answer to a post. So - while we have actually responded pretty quickly - I must ask you to have a bit of patience. Thanks.
Marilyn