If you haven’t tried it already, do a reboot of the Plex Server in case a component has stopped working and needs to be started again. I think you can do a manual Analyze command on the shows after that to try and re-detect openings. If it continues to not work you would probably want to do the Plex Dance with a show you think should be getting intro detected and post server logs for after you readd the series so Plex can look at what’s happening when the files are scanned in.
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