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Similar to this question, but would like to know specifically if there's a way to do this through the iBookstore/iTunes Producer, and what the process might be.

The books are epub2 and epub3, not iBooks Author.

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Yes, this happens automatically.

https://support.apple.com/kb/PH12101?locale=en_US

During the publishing process, you specify whether the book is new or an update to a previously published version. If it is an update, you must provide a new version number. Readers who downloaded your book are notified in iBooks that a new version is available.

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