To my knowledge you can't reset the entire system. Not sure what issues you are having. It varies with each generation, but basically each device stores its own configuration. So resetting the main panel wont have any effect on the UCM or By-Pass configurations.
Probally your best option is to go thru all the configuration settings and verify everything is correct and matches your equipment. Even if there was a way to reset all the devices, you would have to go thru and change these settings to what you have installed as the defaults normally need to be adjusted.