depends how robust the device it I guess, with Sony readers , I've gotten invalid page errors when I've overwritten an existing book without removing it first. Probably because Sony tries to sync the old last page data to the revised book & can't do it
so now If I want to tweak before reading on, I always note the current chapter, delete book from device, send the revised book, jump to correct place via TOC navigation...
back to what OP asks for, I still don't think that it is all feasible, but we'll see
that only way I know of getting complete sync for notes, bookmarks etc even if you read he book piecemeal on several different devices is to stay entirely within the Amazon ecosystem. it can sync anything to anything, so long as it's their book, their software, their hardware and there's an online connection. I don't think its practical for Calibre to work out what page I've gotten to within a book on my Sony device,
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