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https://superuser.com/questions/44812/windows-explorers-file-attribute-column-values
I haven't done an installation of Windows Server 2012 R2 Essentials into an existing Windows Server 2012 AD domain, but I just did an install into a Windows Server 2003 AD domain last week and it worked fine. I was able to join the existing domain, promote my W2K12 R2 Essentials machine to a DC, and then retire the existing Windows Server 2003 DC. It worked out just fine.
Were I in your situation I'd:
Join a temporary virtual machine to the domain (running W2K12 Standard in evaluation mode if nothing else)
Demote the current W2K12 Essentials DC back to being a member server
Move any files off the "C:" volume of the W2K12 Essentials machine you need to save
Reformat the "C:" volume and install the new W2K12 R2 Essentials software as a replica domain controller on that machine
Migrate files back to the new W2K12 R2 Essentials machine
Complete the installation process ending with demotion and removal of the temporary VM
I'd mock this up with VMs before I actually did it, just to be sure it all worked smoothly in real life. It looks like a solid plan to me.
I wouldn't do any kind of "backup / restore" of AD, or any type of AD migration. Using AD's existing replication functionality is the way to handle this problem.