wp enqueue, how to prevent duplication when same script is registered with different handles

JS/CSS Duplication by itself is not bad. It makes the HTML a little bigger nut the browser should in most cases cache the first request and not serve the second one (most cases === unless it is a very badly configured server)

The real problem with duplication is trying to load two different versions of the same file (say two different versions of jQuery), and this is what the API helps to solve by providing a handle to the version which already exists as part of core.

The best thing in your case is to probably think again why do you even need bootstrap in a plugin, why the admin CSS and JS is not enough for you.

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