There is no need to change the TNet's protocol version at all. I don't use it in either Windward or Sightseer. The protocol version only needs to change if you changed something server-side, like adding a new packet.
What I do instead, is have a local game version (Game.version constant for me). When a player connects it checks it against the TNManager.GetServerData value, and if it's lower than required, doesn't allow the player to keep going. The server data value is set by me automatically when I connect to the server after an update (as I am an administrator, so can use SetServerData on connect).