The limits of updating an eBook

This morning I received an email from Amazon, informing me that a recent book I have on my Kindle has an updated version. Apparently because the publication has had significant editorial changes made to it, I need to download a new version.

Fair enough, the ebook wasn't expensive (in fact it was free) and dipping back into my Kindle account doesn't take too long. But there is one issue... because the ebook has undergone significant changes, any bookmarks, notes, or highlights I have made will not transfer across to the new version. Now this wouldn't be so bad if this was a novel or other piece of fiction. However the book in question is actually the Amazon's Elastic Compute Cloud (EC2) User Guide.

This irony wasn't wasted on me and neither was the obvious point that I had two options:
1. Download the updated version of the electronic book and lose my page notes and tips
2. Stay using the old version of the digital guide and live with the discrepancies that predicated the major editorial changes in the first place.

This situation therefore begs the question....Why isn't there a clever way to retain the notes I've made on my Amazon Kindle, even if there are editorial changes?
It was after all one of the reasons I got the thing in the first place! Even if my comments were retained and presented back at the end of the paragraph or chapter... That would still be of some benefit to me.

Note:
Yes, I know that with a paper version of the publication I would have to purchase another updated copy of the book and would not be given the option to simply upgrade it at my own leisure... but that misses the point. We now have a number of ebook systems in use and to ignore my ability to make notes in the margin (as I used to do with a lot of my printed reference material) limits their flexibility and eventual use.

Presumably as more books are digitised and placed online, this situation will become a growing issue. I therefore hope that the vendors such as Amazon eventually find an elegant and workable solution to this problem.