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I've been using the 'EpubMerge' plugin on Calibre. It makes an anthology of the series - so all the books are under 1 title and in order. The name of the new book becomes the series name and I just put Anthology at the end so I know what's going on.
Another idea is to just re-number the series into reading order rather than the proper number order. So instead of 2.1 in your example I would name that 3, and instead of 2.2 I'd name that 4, then 3 becomes 5 etc. Hopefully someone has a proper answer instead of these workarounds.
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