Unfortunately, I don't know when this might have happened, but my CoursePress Pro plugin somehow completely uninstalled from my multisite install. It was missing from the site where I had it activated, so I searched my network installed plugins and it wasn't there either. I have since reinstalled it and my courses are still intact. I haven't been ready to bring in students, but I just sent out invites today. I'm worried that this might happen again and erase student data.
I've got support staff access enabled if you're able to search and find what might have caused it.