What dimasic said is perfectly valid, though

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KindleGen builds combo files, and the user-friendly tools out there (mobiperl, java metadata editor) do not handle those properly: they only tweak the header of the legacy M7 part.
So, yeah, unless those tools are updated, the easiest way is to split the combo file with KindleUnpack, then tweak the KF8.
EDIT: Oops, missed the mention of the Quality Check plugin. Nice! Will have to check how it handles combo files, because that sounds way easier

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EDITē: Nope, same as the other tools, only tweaks the M7 header :/.