If you restore the Jailbreak will be wiped off because Apple is no longer signing any iOS earlier than 6.0. Your iPad will return to normal but everything concerning Jailbreak (apps, tweak, etc.) will be gone. What I would suggest before doing that is the following, I know some will seem obvious if you've done it already just skip it and move on to the next one.
1. Reboot the device
2. Plug the device in with iTunes open and then power the device off, it should power back on and you just want to see if that will force it to be recognized in iTunes
3. Connect it to a different machine, don't sync it that will wipe everything off you just want to know if iTunes on another machine will recognize the iPad
4. If you're running Windows right click "My Computer" choose Manage then go to the Device Manager look for the drivers for the iPad and remove them
Reboot your computer and it should prompt to install the drivers again. Then see if iTunes will recognze the iPad
5. Connect the iPad with iTunes open then unplug the USB and plug it back in or even change the port
I have had the same issue intermittently but usually it's only for a few minutes and eventually my iPhone shows up. If you really value your Jailbreak I would even recommend re-installing iTunes before doing a restore.