The second copy was just to make more space on my eidolon slots.
In the future we"ll be able to sell eidolons for phantom beast orb and can use it to exchange for stuff like event eidolon, kaiser dragoon eido, rings, earring, draconic eye fragment etc..
So i'll save all the extra i can get to have more orbs whenever it comes to nutaku.
And to not fill all my slots with extra copies i just limit break them.