Zombie database entries

I’ve been working on a personal project using the PlexAPI and I stumbled across a bunch of missing files for shows in my Plex DB. Digging in further it seems that I deleted some files for shows long ago, but their DB entries stuck around.

So now I’m trying to figure out how to clean these up. I’ve tried emptying the trash, cleaning bundles, and running optimization. What else can I do to remove these show entries?

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