I had 2 Scala projects open and opened a third one. Everything was going fine and then IDEA told me there were updates available for a bunch of plugins (I don't remember all of them, I did notice one of them was Scala). I told it to update.
When I reopened IDEA everything looked fine. I started editing a file in the 3rd project, and then IDEA told me the file was outside of the project and did I want to unlock it. Since I was in the flow with my edits I told it to do so. All references to packages and classes inside the 3rd project turned red. I then closed and reopened IDEA, and noticed that, in the top where the project name appears, the name was one of the other 2 projects. All files were locked. Going into Project Structure I realized that all the dependencies, modules, etc. referenced one of the other 2 projects.
I then closed all projects and reopened just the 3rd project. It still showed the same problem.
Right now I'll do a backup of the .idea directory (in case this is needed to fix this) in the 3rd project and re-import it from SBT. Hopefully that will fix things, but I am really nervous about this.