Anime episodes no longer "seen" by Sonarr

Hi, I’m not really sure what’s going on so I’ll try to describe the issue as best I can.

I have a lot of anime and a few of the shows I have contain well over 300 episodes. For some reason, with these high-volume shows (and even some of the lower volume series) Sonarr has decided that I don’t actually have those episodes on disk. In the Show view there are only a few episodes listed and the others all show as not being there.

For instance, I have Detective Conan being tracked and the show is currently on episode 768, of which I have about 760 episodes. Sonarr thinks I only have 192 episodes.Dragon Ball Kai, most of the episodes in season 2 are “missing” but exist on disk. same goes for almost any anime that has more than one season.

All of these shows are set to use absolute numbering as well. I have tried going back to seasons and episodes but that did nothing.

Please let me know what other info you need.

My version:
Sonarr Ver. 2.0.0.2939
develop

How are the files named on disk? (an example of a couple that aren’t being detected would be very helpful).