No worries. Typically you can rename a machine by just changing the name System Preferences -> Sharing. But there is also a command line option to adjust the name, and if you don't use the command line option, the server freaks out and will alert you about the change forever. ie - for servers, you need to use the command I describe below.
The command is called changeip and can be run from command line in Terminal.app. It is for manually chaning the ip address and or name of a machine. It basically has 4 parameters: old ip address, new ip address, old machine name, new machine name.
Basically the command looks like this:
sudo changeip OLDIPADDRESS NEWIPADDRESS OLDNAME NEWNAME
If any value is being kept the same, just repeat the identical information as both the old and new value.
Example 1: Changing the IP address and host name. This would update the machine's ip address to be 192.168.1.2 and its name would be update to my_new_name.
sudo changeip 192.168.1.1 192.168.1.2 my_old_name my_new_name
Example 2: Keeping the IP address the same but updating the name. This would update the machine's name to my_new_name but would keep the same ip address.
sudo changeip 192.168.1.1 192.168.1.1 my_old_name my_new_name
Most likely you're just wanting to update the name, in which case you should follow the second example. If you run this, be sure to reboot the machine afterwards and test to make sure that any enabled services are running properly.