Disposing of Helix Viewport and contents

Is there a way to dispose of these ?

My problem is this....I have two windows. One does operations on files and the second window shows the model in the viewport.

Even when I close the second window with the viewport, the system still has a connection with the files previously used by the viewport.

So when I return to window one I get an error that my files are already being used (by window two).

I thought using Close() on window two would clear things, but it does not.