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under comic input there is an option to preserve color, use it. But remember that the Kindle doesn't display color.
The resolution of the images in the MOBI file will depend on what output profile you have chosen.
I'm not sure what you mean by pages being lost. WHatever images are in the input CBZ will be in the output MOBI. (Just make sure the images are all in the same directory in the CBZ)
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