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OK, now I tried it at home with the same files and everything works fine. (Debian, Calibre version 0.8.41)
So I guess the trouble will be Windows-related. Now that I know how it's supposed to work I'm adding that the moment things went wrong, in both cases, was at the moment I selected a file to be merged and clicked the button, before the other dialog is displayed (the one where I can choose whether to merge the whole file or just the annotated pages - I didn't even know there was one).
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