If you update using iTunes or over the air via your iPhone.
the update will be coming from Apple and legitimate. If your
update source is not one of those 2 items, then no one knows
what software you are getting and what damage it will cause.
Applying a legitimate update to a jailbroken iPhone does not
necessarily return the iPhone to all Apple software and the
remnants of the jailbreak probably will cause problems in the future.
Is there something that occurred causing you to ask this question?
How did you update your iPhone?