I have inherited an Active Directory environment that is at the Windows Server 2003 forest and domain functional level.
The DNS domain name has no special characters--it looks like sampledomain.org. The NetBIOS domain name has an underscore in it and looks like sample_domain.
Some have told me that because of the underscore, this domain cannot be "upgraded" to Windows Server 2008 R2.
Documentation that I have seen on TechNet seems to simply state that a DNS domain name cannot have an underscore in it. I see nothing that states the NetBIOS domain name would prevent me from upgrading to 2008 R2 domain controllers and raising the forest/domain functional levels.
Which is correct?
I'd go with the docs on this one. Some scanning on my own of the technet fora likewise shows this to specifically not be a problem.
Worst case - try forestprep and domainprep and let them try to complain. No complaints -> no problems.
It is entirely possible to have a NetBIOS name different from the first label of the DNS's full domain. At my old job, we had the following (changed):
Logins could use either "EXAMPLE\username" or "username@ad" syntax for login prompts, and technicians could use either "example" or "ad" for the "Domain" line when domaining a workstation. Just before I left we managed to get it to the 2008 functional-level. You shouldn't have problems with an underscore-bearing NetBIOS name.
I recommend using a virtual machine to create an isolated AD DC with a similar config (keep it off the network.) Attempt to upgrade the VM.