I, inadvertently, did the same thing yesterday. I was implementing new STIGs for Server 2008R2 and 2012R2. Did a bunch last week and all was looking good. Still had 15 more to fix based on Nessus scan so I looked at what they were and realized some I had already corrected (or thought I had). Most were ones that required you to deny Domain Admins, Enterprise Admins, and Guests from having login/remote/batch/service access.
Some commenters wanted to know what GPOs caused the problem so here is what did me in; Computer config-> Policies-> Win Settings-> Sec Settings-> Local Policies-> User Rights Assignments. There is Deny Log on a batch job, Deny log on locally (be careful), Deny logon through remote desktop services (be careful), and Deny access to this computer from the Network (this one did me in). There are also settings to allow some of these same rights but if you deny them, the allow doesn't overwrite.
I added Domain Admins to the GPO which already had the Guests and Enterprise Admins groups. This GPO was applied to all servers (including DCs). I was hesitant to do it but needed to test to see what would happened. Within 60 seconds of closing the GPO edit window, everything broke. No 90 minute wait for Group Policy to update. No reboot required to implement the computer policy. Things just broke, quickly.
I tried to make the boot CD or USB to edit the DSRM Administrator account to no avail. So, I used what Wilson mentioned above, edit the policy and change revision number. Worked perfectly after booting from the Server 2012R2 install disk and selecting repair. Then selected Advanced Tools and Command Prompt. Found the files, edited and saved them. Rebooted and still couldn't login but was able to remote in from a workstation. Disabled the bad GPO and rebooted the server. Everything is back to normal.
Biggest problem was all our Admin folks are in Domain Admins, I know it is bad practice now but some people are hesitant to change. Clearly we will create new groups and assign people only to the groups they need. Then use GPOs to give those specific groups access to what they need so we can still implement the STIGs.
Hope this helps!