If you opened the subVI when the main VI was not open, then made your change and saved the subVI to a new filename, the main VI will never know about the change. In this case, you can open the main VI, right click on the subVI and select Replace->Select a VI... then browse to your new VI and select it.
The other solution is to open the main VI, then double click on the subVI, make your changes and then even if you save it to a different filename, the main VI will be linked to that one.
Rob