Hi @OBHSDonohue,
From your description, my guess is that something may have changed in your student information system (SIS), causing new courses to be created in Canvas and the enrollments of the teacher (and assuming students too) to be moved to the new courses. The things that lead me in this direction are that the courses are unpublished and empty. Once anything in a course is graded, it should be almost impossible to unpublish it. If these are all brand new courses (probably with the same title as the originals), that would explain everything you see right now.
Now if this is the case, the trick is going to be to figure out what changed in the SIS, and then figure out if the change can be reverted or not. I would start with looking at whatever field maps to the Canvas sis_id.
If you can find and revert the changes in the sis, Canvas should be back to normal the next time a sync runs.
If you can find the change but can't revert it in your sis, things are going to get much more complicated... You may be able to run a provisioning report in Canvas, including deleted items), to find the original course shell id. You could potentially restore the course shell if its been deleted, then start changing around sis_id numbers between the new course shell and the old one, which may get the students back into the old course shell at your next sync and restore all of their assignments and grades. I have had to do this a couple times in the 10+ years we've had Canvas, so it's an exceedingly rare set of circumstances where it becomes necessary to do this for us.
If you can't find any changes at all anywhere, maybe someone else here would have some other ideas.
-Chris
