I am having a problem with re-loading a specific project. The first open is good via File->Open menu. Then I quit Xcode and restart it. Now the project reloads, but the Project Navigator only shows "PROJECT NAME.xcodeproj" in red without the normal project folders/files tree. All other projects are good. I think this problem started from version 9.2.
I reported the problem at bugreport.apple.com and got a positive reply from Apple engineer:
It looks like you have encountered a known rare issue when creating your project. You can repair it by opening “swiftsandbox.xcodeproj/project.xcworkspace/contents.xcworkspacedata” in a text editor and replacing "self:/Data/Build/Xcode/sandbox/swiftsandbox.xcodeproj" with "self:swiftsandbox.xcodeproj”, that should resolve your issue.
But the bug is still active in the latest version 10.1. Hope this information can also help others who have the same problem.