Hi,
I had downgraded back to 6.12.8 and the "bug" is gone. I also notice that i had some problems with new episodes that's has been added to Sonarr. Some of the episodes wouldn't be added even when the episode was in the right season folder. I deleted the episode, redownload it. It was added to the right season, Sonarr found it and everything seems to be ok,. But after I did "Refresh & Scan" the episode was gone from sonarr, but i was still on my NAS.
Rolled back to 6.12.8 everything back to normal and no more problems with episodes in Sonarr.
All my Media files are located on my NAS, so all the arr and plex server are pointing to my NAS.
So I stay for now on version 6.12.8. Maybe some other are experience the same when they have the same setup like I have.