We are planning to upgrade our ArcGIS Server and Portal for ArcGIS 10.3.1 installation to Enterprise 10.5.1 and use a new VM with Windows Server 2016. I'm thinking of using the Enterprise Builder tool to create the site, since it's supposed to make the 10.6.1 upgrade easier. Is there a way to copy the existing Portal configuration to the new 10.5.1 Portal? Also, can I use ArcGIS Online Assistant to copy the content from 10.3.1 to 10.5.1? As a side note, we aren't upgrading to 10.6.1 quite yet because we will also have to upgrade ArcFM to 10.6.1, so that project will happen next year.
If you are migrating the ArcGIS Enterprise from one machine to another with new machine name, you will have to install the software on the new server machine and then re-publish all the services.
There is no documented workflow to migrate services from one machine to another.
You can use the Enterprise Builder to build the new 10.5.1 version. All the software will be on the same machine. And when you upgrade the ArcGIS Enterprise to 10.6.1 you can use the Enterprise Builder 10.6.1 version to upgrade.