It sounds like you intend to look into it anyways but I would +1 something being there for it. I confess to not having read your post in detail and you obviously know the issues better than anyone. From my "end user" perspective, given that I have already got the ability to specify what Kindle collections are to be preserved, I think anything outside of that is fair game to be blown away by your plugin. My fear is that if you bend over too far to try to be flexible for every situation it all just becomes too complex to use and know why collections appear/disappear.
Again this is based on a simplistic ignorance view - but surely if a user specifies what collections they want to keep (as you have already got the ability to do), it is perfectly reasonable to assume that anything else can be overwritten/removed?
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