I keep having issues with sonarr deleting episodes. I have set everything up properly with sabnzbd and sonarr does the moving and renaming (succesfully), only to directly delete the episode.
According to the log that is because there is a better file available, but the better file doesnt get downloaded. I’ve seen others with the same problem on this forum, but I couldn’t find an answer (only closed topics).
Sonarr doesn’t delete a file for an upgrade unless the new file is already on disk.
Also make sure the issue isn’t present because sorted and unsorted files are being put in the same location, that can cause all sorts of issues (a lot is being done to prevent this).