How do I update an iBook created in iBooks Author without losing old notes?

I have been creating an iBook using iBooks Author. I export it as an iBook that I can open in iBooks on my computer and on my iPad.
The challenge I am running into is that I highlight sections and make notes and want to keep those even as I add new content to the iBook. Is there a way to update an iBook on my computer and have it update the one in iBooks without losing everything I created before?
Thanks.

AFAIK, the update process that allows note/bookmark retention is currently only thru the store.

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