Rename the system in your FL (or delete it if you know in your head of any changes you've made), add system from full db to your FL, apply your changes, delete old renamed version of system.
I guess if I had to do this every week I'd worry about this complexity, but I don't apply updates to my FL unless I know there are significant changes that need to be made. IMHO, what would be nice is a tool to do a side-by-side comparison of the two versions of a system, highlighting any differences and allowing you to apply the differences to your FL or ignore them.