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start over.
delete what is in calibre. configure calibre to view mobi with its own viewer, or install kindle for PC , or both.
add teh book to calibre - you now have a .mobi format book
view it with calibre / with kindle for PC check that all is Ok with chapters & navigation.
then redo your book cover changes. ( that is in edit metadata I assume)
then reconvert mobi to mobi - double check all settings - the one most likely to mess with chapters is having heuristics turned on.
view the output of that stage on PC.
if OK, then send to kindle, but I would delete the original from kindle before placing the new version on there ( or change the title ) so that Kindle is not being confused by an overwrite of what it had before ( it shouldn't be , but its safer to rule that out ). you can always retrieve your amazon original from amazon archives.
to be honest though, K3 makes such a poor job of displaying book covers I wonder why you are bothering ? - you can only see covers on K3 by selecting book then right arrow, or by opening book at start followed by left arrow, and the former only shows a tiny black n white thumbnail .
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