I don't have a kindle, but as I understand it you have to use a "plugboard" to update the title metadata when you send the book. The reason is that mobi format has no support for series metadata, so it has to be put in the title instead.
The best way to do that is by using a plugboard. That way you can use all the fields in Calibre as intended, and automatically get the title updated when you send it to your device.
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