Nothing you need to do at that point. When you restart the unit you should do a "Restore Factory Effects Presets and System Settings" as described in the UM. This WILL erase all user presets.
User Presets must usually be recreated because they are often incompatible with the updated system. It's worth backing them up before the update and giving them a try, but tweaks are usually necessary. For example, if, as often requested, we change the range of a control, previous knob settings will be in the wrong place.