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Your main problem here is not merging databases (that requires manual work anyway, as there's no automated way to do it), but removing the DRM from all your books, if you decide to import them into calibre. While it's still pretty easy for Google Play books, it's no longer so easy for B&N and Kindle books, and requires jumping through some hoops. Plus Amazon is actively trying to stop DRM removing, so if you wait too long, you may no longer be able to do it at all.
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