One thing I have seen with using projects is that the "nested" Playback optimisation files for the subprojects can get confused. However, you have said you have deleted the render files so this should not be a problem, unless at some point the render files location had been changed.
With the new sub prohject handling it's not too time consuming to open up a timeline project by double clicking, switching to the new tab, copyig the contents, switching the tab back to the main project and pasting the contents below the subproject and then deleting that - effectivly putting the original project on the timeline. I wonder if you just replaced the two troublesome projects with their real selves it would bypass the issue? Not a solution,I know, but might provide a clue, particualrly if the export still hangs.