I think the short answer is With Difficulty.
You can go through each of the books on your device and re-do each of the highlights, notes and bookmarks you've set in there.
Obviously if you care about the data, you need to back it up regularly. I'm surprised there's no calibre plugin to handle this (at least I couldn't find one).
Quote:
Have you heard of Kindle Mate?
You can see if this program reads your notes and highlights.
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I had not.
I don't care at all about
My Clippings.txt (would like to disable it actually), but I didn't know
Vocabulary Builder data was accessible. I have long wished that Amazon would sync that data between Kindles (and add the feature to the Kindle apps).
It seems it will do a manual sync. Cool.
However, Windows is not very convenient for me. I have a couple such machines but rarely turn them on. One of them spends half a day updating everything when I do, and I have to sit next to it and listen to its loud fan. The other is a netbook and Windows 10 barely runs on it. I'm not going to create a Windows VM and purchase a Windows license to run it.
I see there's a thread here for questions, so I'm going to head over there and ask a few.