Restarted the device, launch the Pangu app and click jailbreak then lock your home screen. Your device should reboot soon, you'll either get a pop up saying 'Jailbreak was successful' or get direct reboot without any pop up. If you don't get any, that's a fail JB. So do the same thing and this time, try to wait from 8-20 seconds before lock your screen. Simply put, you still can JB your device even after reboot though it might take more than 2-3 reboot to get it back.
Worst case scenario for me was restarting the phone and see that my JB profile was gone and I can't launch Pangu app at all. That was when you had to restore your iOS version via iTunes to 9.3.3 and Re-JB again. I notice that 'reboot' from Cydia won't do anything but try shut down and turn your phone on again might cause this issue.