I’m sorry this happened to you, but you should simply not upgrade the Plex server on shield as long as you can. Because when things go wrong (and they do go wrong frequently), the shield server is not at all well supported by Plex.
2 years ago there was another bug where it couldn’t connect to a directly attached external storage drive, and it took them MONTHS to resolve such a critical bug. Another recent update caused this: SHIELD Plex Media Server suddenly stops searching for content automatically And then after months of no replies, the thread was simply closed.