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@JohnPhilpin I'm leaning towards @manton's power is needed for this kind of problem.
Skimming the sitemap.xml, I count 4,911 posts and pages but only 16 replies. @pimoore's theme should only affect the presentation of replies. I don't think it's to blame for the missing ones.
You could always try turning it off and on again. 🤭 That is to say, forcing a complete rebuild of the blog. Sometimes, that will chase away weird issues like this.