My project was created in Xcode 3, I\'m opening it in Xcode 4 and notice the following:
I fixed the problem by removing derived data in th Organizer, running touch MyProject.xcodeproj/project.pbxproj and re-opening the project. After re-opening it, it started indexing and then it was working again.
touch MyProject.xcodeproj/project.pbxproj