I have done this many times with going to 2012 but going to 2012R2 caused an issue that I don't know how to fix.
This is for a client that has one file server that is 2003 and needs to be replaced.
The steps that I take are:
1) Install 2012server
2) Add ADS Role on 2012
3) Copy files and folders from 2003 to 2012 server
4) Transfer FSMO roles
5) Shutdown 2003 server
6) Run metadata cleanup
7) Change IP address on 2012 server to what 2003 server was
8) Rename 2012 server to same name as 2003 server
9) Setup shares on folders for 2012 server
The issue is that when I went to rename the 2012 server to same name as 2003 server it said that it could not do that and then told me I had to reboot.
After reboot I had on the new server the name of the new server but it would not be recognized by that name. Instead it is recognized by the old name.
I put the old 2003 server in place and seized the FSMO roles back. Removed the temporary 2012 server name from AD and DNS. All is working fine on the old server.
I completely removed everything from the new 2012 R2 server (AD DS, DNS, demoted the file server) then I put a different IP address and gave it a completely new name.
I redid steps 1 and 2 and both the server see each other.
DNS is working. I checked it by adding a new user on the old server under AD Users and Computers, found it 5 minutes later on the new server AD Users and Computers, deleted it from the new server and it was deleted from the old server 5 minutes later.
My question is when I get to the step to rename the new server to the old server's name, is there a special way that I am supposed to do this?