From time to time I delete old season from the disk manually. Sonarr does not detect that these episodes are gone. It still lists them as if the file still existed. Yes I did clicked the “Scan Disk” button in Sonarr. Newest version. Mono 4.6. Freebsd.
Sonarr won’t rescan a series folder if it doesn’t exist at all, if it exists and is empty Sonarr will rescan it and see the files are missing. Sonarr won’t treat a missing series folder as having no episodes on disk to avoid issues where a mounted share or removal drive is not mounted.