I understand from very little that I know that I have to uninstall this IDE and install the new version (1.8.9).
I also have installed core for ESP32 from GitHub by using method described in the Readme md, by the Git clone and Git bash method described.
My question is how do I upgrade so that I do not have to re install the cores and boards already installed in this version.
You can do as you like with the Arduino_1.8.8 folder. Probably, you'll just want to delete it. However, the "Windows ZIP file for non admin install" version of the Arduino IDE allows you to have as many versions of the Arduino IDE installed at the same time as you like so you can keep it around if you want. I currently have 37 versions of the IDE installed on my computer, but that's only because I need to be able to use the same IDE version as the people I'm trying to help here on the forum, and because it's useful to be able to do backwards compatibility testing for software development.