Updating iPhone with Jailbreak?
If you do an OTA update on the device, you'll 'break' many things and the device probably won't boot.
If you do an update through iTunes, it may boot, but the jailbreak will be broken and the filesystem may be a bit messed-up.


Basically, don't update your device.



Instead, you need to wipe and restore your device.


Make a backup of your device in iTunes (I don't trust iCloud backup with jailbroken devices).
Restore your device using iTunes.
Restore your backup to the device using iTunes.


The backup will contain many preference files for various Cydia tweaks, but they're fine to leave since the actual tweaks won't be there (it's not jailbroken any more).

You should end up with a non-jailbroken device with all your content excluding content for tweaks.