Doesn't surprise me any, frankly.

Things fall apart, the center doesn't hold, mere anarchy is loosed upon the development environment.

Some internal item got messed up. The actions you took got it unmessed (or is it messed down?). In any case, it went away, and will likely stay away. I've seen this happen before with VS, though never this exact message. I do have one project that periodically forgets about a sub-project within the solution. Your solution seems about right.