Yo, I've found that notes can be kept by manually copying the .PDR file that is in the same folder as your pdf. Let me give you an example:
BLAH.PDF BLAH.PDR
I've only tried it within the same kindle but it has worked for me. I've yet to test it using two Kindles, and also with highligths.
Although I've noticed that some PDF don't display highlights properly in the "View Notes and Marks" screen, so I didn't bother with something that might not work properly.
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