An update - I finally had a day free to tackle the corrupted Linux filesystem. I attempted to restore a system snapshot using the TimeShift utility but sadly the root system file ownership error persisted, so I was forced to wipe the drive and start from scratch.
Thankfully I had hundreds of pages of notes from my last system build so I was able to follow my process guide troubleshooting various new version bugs along the way. In 4 hours' time I had restored all my applications and their respective configurations.
It then just took the rest of the day to re-index my media server. So far... so good.
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