Hey,
Sorry I just came across this now, but I've had the same error too, so I'm sure others have. There was a quite a bit easier solution than what you had to do, at least in my case. I had the exact same problem, where my main project said there was an error, so I couldn't debug or run, but there was no apparent error, other than the red X on my main folder.
In order to solve this, I simply closed the project by right-clicking on the main folder, and selected "Close Project". Then, I right-clicked on the closed project, and selected "Delete". Don't worry, this will not delete any files, it will only remove it from the workspace, and will make sure you really want to do that by asking you to confirm. Now, just click on File->Import and select "Existing Projects into Workspace". Choose your parent folder for your app that was erroring, and import it. The few times I've had the phantom error on my main app, this has fixed it each time.
Whether there is an underlying cause and this process simply refreshes something in the workspace, I'm not sure, but at this point this fix is fast enough for me to use it.
Hope this helps next time!