In your Leanpub library and the Leanpub app, we overwrite the file. If you want old versions, you need to store them yourselves.
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We don't automatically add to iBooks, you do that yourself.  So, when you download a new version, you just add it to iBooks again.
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You always get the entire book, not just new files with new instalments. The reason is that authors can edit whatever part of the book they want, not just add new things.