The good news is the update won't trash your node.prp file and other settings.
Well except the NSUIElement key that you may have changed for Jaguar.
Obviously if you have 2 installs, one with a different name, you will have to manually update the new app to have your changes from your original second install.
I would just backup the second client somewhere, rename client 1 to something other than the default, rename client 2 to the default(SengentD2OL.app) and then run the installer. Then rename client 2 back to its original name and make the changes you need to the Info.plist and Executable name.