We stopped to split KindleGen output on KCC level due the fact that creating AZW3 file from hybrid MOBI when it have several hundred MB can take minutes (on even more on old hardware).
@flat__line - You have two options. Split it like @kovidgoyal said. As long you don't make AZW3 -> AZW3 conversion in Calibre they should not fall apart.
Or use ComicRack metadata support in KCC itself to set all data you need.
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