I’m just trying to determine if this is in fact why I’m seeing this behavior and if there is a way I can prevent it.
I schedule my NAS to turn off during the day when I’m at work. No sense in having the thing running if I don’t need to use it.
I find that some shows that download the night before, download again when the NAS comes back on at 4PM the next day. When I click on the Series section all the shows will show as 0/xx episodes as well. Until what I assume is a library refresh is performed. At this point is it possible that it downloads those episodes again? I’ve checked and they’re not propers. They’re the same episodes it already downloaded.
In Sickbeard, it would show you that the source directory for the show is missing but not 0/xx episodes.
This is the behavior you’re seeing: https://github.com/NzbDrone/NzbDrone/wiki/FAQ#why-does-nzbdrone-refresh-series-information-so-frequently
The disk scan sees the file as missing and removes the files, and they are treated as missing, which is why they are regrabbed.
Currently there is no way in drone to alter this behavior, it would have to be implemented. Workarounds: either to sleep the PC running drone or shut drone down.
Have to ask, why bother shutting down your NAS (generally a lower power device), but keep the computer running drone on?
I see. Well at least I have an answer and know it’s expected behavior. 
Shutting down my NAS is less of a power saving issue as it is wanting to reduce the wear and tear on the fans and drives in the NAS from running 24/7/365. I leave the PC on because I remote into it from work but I don’t do anything on it that requires the NAS to be on during that time.
I might try shutting nzbdrone down before bed. Or I might have to switch back to Sickbeard. 