Figured it out. Evidently just replacing the file isn't enough, even stopping
and restarting services. I guess you have to have an existing something
already set, maybe to make media center "aware" of the file or something. As
soon as I scheduled something, checked that it was really scheduled, stopped
the recording service, replaced the file, then restarted the recording
service, all my shows were there again scheduled correctly.
So schedule something, *then* replace the file with the backup.