I guess what I am asking is does the install process copy files from the new version and overwrite the older version files?
Or do I do that,
I am confused about what you are doing??
There is not an automatic file upgrade in zc_install
You stated earlier that you had a test install
Have you/are you following the upgrade tutorials?

https://www.zen-cart.com/tutorials/index.php?article=98
https://www.zen-cart.com/tutorials/i...hp?article=108