I have seen on pc iTunes the button to "restore iPad" ... After the hopefully successful jail brake, how we re-load everything was backed up in the pc?
that "restore iPad" means, it will restore to a stock firmware again(jailbreak gone).
this "restore from backup" is what you need!!
right click on your iPad in iTunes in left pane(pop up window appears).....
when you are jailbroken, don't restore or update iPad.
Sync all you want!!