Why not just have two separate installations of TNet server on your box?
Each game uses its own port. Could recompile TNet for unique game ID, too.
Maybe I'm misunderstanding what you're trying to do. TNet uses a single game ID for verification. You could modify this to include multiple game IDs, but for what I think you're trying to accomplish you'd also have to rewrite the lobby server and channel logic to accommodate multiple game IDs on a single server instance.
Really it's probably just best to use separate instances, but maybe ArenMook can chime in.