This error message occurs when your installation is not at the place where Netbeans expects it to be.
Now you've written s.th. about uninstalling and reinstalling everything. Maybe that caused the problem. You can see at what location Netbeans expects the domain.xml to be in the Server Manager (Tools -> Servers). If you highlight your Glassfish instance there is an entry called "Domains folder". Maybe the folder given there is not the same folder where your default domain has actually been installed.
If all seems to be correct I recommend removing this server (in the Server Manager) and directly add the actual instance of Glassfish you are using again. This might help in case any other configuration Netbeans expects has changed.
If the problem still exists after removing and re-adding Glassfish in the Server manager, you might also try to get help in a Netbeans forum.
BTW: You will not see anything relevant in the file server.xml since Netbeans couldn't contact your server at all!
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