IntelliJ sometimes gets confused all by itself, even without the external changes Korgen described (though that is a good way to consistently reproduce it).
Click File -> Synchronize, and IntelliJ should see that everything is okay again.
If that doesn't work, IntelliJ's caches might be corrupt (this used to happen a lot more often than it does now); in that case, regenerate them by
Clicking File -> Invalidate Caches and restarting the IDE
(though loading the project will take a while while the caches are recreated).
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…