We understand this as one of the shortcomings of the folder structure.  In order to keep the tree up to date, we are forced to refresh the tree, and there is currently no functionality that allows us to remember the state of the tree before it's refresh.  As we improve Contour, we are slowly moving away from the tree as the sole means of a project's perspective.  We hope that features like tags, filters, and set views will eventually replace the tree as the prefered method of interaction with a project. 

Trees have many natural shortcomings, and we feel that technology in general is moving away from these types of interfaces.  A couple of examples of this would be Mac OS X's spotlight, Linux's Beagle search, and the tag / category features of most blogging web apps.  That being said, the tree view will be with us, and continue to improve as time allows.  While the tree refresh is not currently on our roadmap, we are working on several other features that should help making browsing more user-friendly, and more intuitive.