Sometimes I accidentally close Geary, when this happens I reopen-it as soon as possible, just to see it close itself a few seconds later.

I suppose the window is simply closed while the app is stopping properly in the background and it's good as it make the application feel snapier, but seeing the application window close itself just after you open it is really not the best experience.

I suppose a somewhat simple way to fix this would be open the new window while the application is stopping, to display a loading state in the window while stopping Geary, and instead of exiting the process the app could be seamlessly restarted in the already open window. That would just appear as a slightly longer stat-up time to the user.