unless you save site options from before an update this causes problems.
Are you using a child theme?
because if not! when you update a theme it will basically cause you to have to do major rebuilding.
I always set up as the activated theme a child theme. this way i can update the master theme when it updates, and I never touch the php code in the main theme.
I will have the child theme running/activated and all changes are made to the child theme. Then when a theme updates I will save these changes to the child, and reapply them to the new updated child theme once it is set up.
Assuming that you did not have a child theme in place prior to the update you will need to make all of the previous modifications to the new updated theme.
consider very importantly to utilize a child theme for your site.