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You're talking about two entirely different things. If a file is already split into multiple flows, Calibre won't re-merge it into a single flow, it will convert it as is, possibly adding new split points if configured to.
If a file IS a single flow, there are a variety of ways you can get Calibre to split it during conversion, one of which is the preprocess option combined with page break settings. The bug I fixed was to split files, not put them back together.
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