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@MerlinMama - Suggestion: when you get this problem, copy the epub somewhere, then open the copy in the editor (it'll be a second instance) and see what happens if you only redo the edit that just did the unwanted paragraph re-ordering.
If it reorders the paragraphs then that probably suggests there's something in the 'book code', that's causing the re-ordering. I can't imagine what that would be. But you will at least have something repeatable that Kovid could look at.
If it doesn't reorder the paragraphs then that suggests either it's something you did, or its something in the book editor that only manifests itself after 'extended' use.
Its instances like this where macros will be handy. I often make a mistake when repeating a familiar sequence of operations.
BR
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