Hey folks, I wrestled with this all day and finally got it solved. I use an UNRAID V6 for my media. I recently switched from mounting via SMS to AFP. I don't know what exactly was going on but when the AFP shares were scanned for new media, it would find it all, then start deleting roughly 400 movies from Plex. The movies getting removed were random. The same film rarely got removed twice. I switched from AFP to CIFS (much faster than SMB on my Mac) and the problem was resolved.
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