The upgrade and copy to a new enterprise geodatabase (EGDB) are not the same. It is possible to do either.
Upgrade = keep everything in tack and place (permissions, versioning, replicas, etc.) and bring it to the latest version.
Copy to new EGDB = Copy the data to a new GDB via ArcGIS Desktop client. This will NOT bring over the permissions, all the versions of data and/or replica information (if you have that enabled and in use). This will also not include any special keyword configurations that you have in the older EGDB.
When you copy over the data it will bring over the data version that is copied. You will have to do more configuration on the "new" EGDB once the copy is complete.
My follow up questions is this: What is the thought behind coping the data over to a new EGDB vs. Upgrade in place? T
That may help with some of the response.
--- George T.