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There's a couple of omnibuses I've not split, but that's because the structure of the file means there's no break point. Otherwise, EpubSplit is your friend, especially as you now can mark common sections so you don't have to keep re-selecting them.
What I've also done for series with sub-series (or a connected universe) is to use custom columns for the sub-series and have a meta-series as the main series. Examples here would be the Foundation Universe (different series at different timelines), or Alan Dean Foster's Humanx Universe which have braided series. I find it useful to have the meta-series in date order (easy to identify the date with Humanx, not so easy with Foundation), then it's trivial to slot in new volumes.
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