I found out you can do this pretty simply. I wanted to change my 2012 R2 Standard Eval ISO to use my 2012 R2 Standard MAK key. I ran this in an elevated command prompt:
DISM /online /Set-Edition:ServerStandard /ProductKey:xxxxx-xxxxx-xxxxx-xxxxx-xxxxx /AcceptEula
replacing the x’s with your key, hit enter and it should work with a requested reboot right after it completes.