I'm having the same question.
It seems the XLIFF file is not updated in terms of resources.
Does the issue occur in the latest update? It works as expected here. It should not open in the next session with the same project after closing its tab.
The latest update seems OK!
Hans CafeTran Wiki
When you close a resource in the tabbed pane or uncheck it in the Dashboard, it will nevertheless be loaded again when you start a CafeTran project again, in which you previously opened this resource.
In other words: the resource isn't removed from the XLIFF when it is unchecked/closed in the tabbed pane.