There is no simple way to retain changes made to the secondary. If you try to sync them back to the primary later, other things may break unless you're careful (e.g. fix CARP VIP skews, DHCP failover IP addresses, etc)
If you know the primary node will be gone for quite some time, just grab a backup off both units, power it off, restore the primary backup file to the secondary, and now you just took your "secondary (formerly known as the primary)" is down for maintenance. :-) When the time comes to switch back, you could either restore the secondary node config to the repaired unit or swap them back around.