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One idea (and I've spent less time thinking about it than writing this post, so take it for what it's worth) is to keep both the original and modified versions of the books in Calibre as separate records.
You might have a separate library for your originals and modified versions for specific devices. Or you might use Virtual Libraries. Or just set up a field to track which is which.
For instance, set up a custom tag-based field to store values such as "Original" and "Kindle". I say Tag-based because it's likely most of your original books will also be Kindle-ready, with only a few exceptions. You'll want to be able to mark a single book as both. This also allows you to prepare special versions for other devices in the future. Then, any time you want to transfer books to your Kindle, use the tag browser to filter only Kindle books so you'll know you have the right versions.
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