So I finally found the solution how to get the updates.
This is what happened:
The server had to be reinstalled with a fresh copy of Windows Server 2008 R2 so I took the original DVD and installed it again on totally new harddrives (the old ones were damaged due to the attack).
After installing Win Server 2008 R2 it couldnt upgrade because of a Microsoft Update code 80072efe error.
The best solution was to first upgrade Windows Server 2008 R2 to Windows Server 2008 R2 Sp1 (service Pack 1). This can be done here:
I downloaded the .exe-file and then installed and rebooted the server.
After this there was still the Microsoft Update code 80072efe error.
I then updated the Windows Update Agent. This can be done here: https://learn.microsoft.com/en-us/troubleshoot/windows-client/deployment/update-windows-update-agent
I downloaded to the server in x64-version. I then installed and then rebooted the server again.
After this the code 80072efe error was gone and after a (long) while it started downloading 1,4 GB updates (I guess more will follow later).
I hope this will help somebody facing the same situation
All the best, Hans