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Many of us prefer a new page for a new chapter (provided they're not extremely short chapters of 150 lines or so). This prevents having page breaks at odd times in the middle of a chapter. Large single files are also known to slow down most ereaders.
If you open the epub in Sigil, you can easily merge pages though. I'm not sure how well the epub merge plugin will work on files within one epub... I thought it was more for combining separate epubs into one (I may be wrong about that though, I haven't played around with it yet).
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