I had the same problem and was unsuccessful in solving it through the control panel, but I did solve it through the web interface. The control panel only controls how this device syncs with the cloud, so it can't remove folders from the cloud.
Both answers offered so far seem to misunderstand the question, so here is a clarification of what I believe was the original problem:
Let's say that inside
~/Parent/ you synchronize
~/Parent/child2/, but not
~/Parent/child4/. Now you want instead to synchronize
~/Parent/ along with anything I put in there. But when you try to synchronize
~/Parent/, you get an error saying it overlaps with other things you've synchronized. You can stop synchronizing each of these folders through each device's Ubuntu One control panel, but the control panel cannot remove the folders from the cloud.
The solution is to forget the control panel and to log into https://one.ubuntu.com/files/, click on "More" to the right of each child folder, and select "X Stop synchronizing this folder." Ideally, you should now be able to synchronize the parent. But for me this never works unless I restart the sync daemon (from terminal:
killall ubuntuone-syncdaemon then
ubuntuone-launch). Then I can right click on the folder I want to sync and select "Ubuntu One > Synchronize this folder".
Maybe the developers will figure out in the future an easier way to synchronize the -parent folder that just includes all the already-synchronized child folders by default.