If you create a custom dashboard theme within the editor it should be saved in the flow file itself so it is present next time you start. So if you are providing a pre-done flow file there should be no need to mess with defaults.
If you really do need to then you need to fork the original dashboard project, edit the theme.less file and rebuild the package (using gulp). This will then recreate the .min files for you.
This is hardly beginner level stuff though.
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