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I am a bit confused - when you plug in a Kindle you should be shown (in the device view at least) what is on that specific Kindle. The library view will always show what books are in the current Calibre library with the onDevice column indicating which books also appear to be on the currently connected Kindle.
I am also not quite sure what problem you are trying to solve? Presumably tracking what books are on what Kindle? Calibre does not normally track devices so if you want a permanently visible way of telling what is on a device even when it is not connected you have to take some actions to achieve this.
What is possible is to create a custom column and populate that with appropriate values. Another approach is to use special values in the tags colum.
A different approach is to use the Reading List plugin to maintain lists of what is on each device. That has the advantage that it can also be used to queue up books for the next sync of that device.
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