Updating won’t remove the jailbreak. It’ll only result in a boot loop. Make a backup in iTunes and then restore your device to factory settings.

Does restoring iPhone delete Cydia?

You will be using iTunes to backup and restore your device to its factory state, removing the jailbreak and all traces of Cydia. You will lose all of your jailbreak tweaks, but you won’t lose any of your data.

How can I remove Cydia from my iPhone?

Open Cydia from your iPhone/iPad. Click on the “Installed” tab and tap on the first tweak that you wish to uninstall. Now tap on “Modify” on the top right and select the option “Remove”. Instead of tapping on “Confirm”, you need to select “Continue Queuing”.