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I can't imagine why the epub format is being deleted, someone with more knowledge will have to help you there.
As to the sorting, try this and see if you can see how calibre sorts the books into iTunes. In iTunes, under the view menu, there is "view options". Select that and you should be shown a list of different items to view in your iTunes window. Select "sort name". That is where the sorting by number and series will show. You can also see this information if, with a book highlighted, you go to the file menu and select "get info" (Command I) and go to the sorting tab. In iBooks, when you view your books by category, if there is a series, it will show the series name as the category, otherwise it will be what you have the book tagged. If it is in a series, the books will be in order from first to last. I really like how this works!
And I just realized, this is how you would do this on a Mac, I have no idea how you would do it on a PC.
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