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I don't think that would work since I don't see how the Minerva could even use the METEORS for the Strike Freedom and Infinite Justice.
If anything they would just upgrade the Eternal if they want a ship that can hold that stuff as they already can.
It also isn't a good idea to keep all your high powered stuff together during peace time and considering that Shinn and Lunamaria are still pilots I'm sure they're going to be doing more than just sitting around waiting for the Eternal.
So if the Minerva was rebuilt I can see it carrying the Destiny and Impulse than having them, and Shinn/Lunamaria, transferred to the Eternal later on in the Movie for whatever plot reason. Same for Athrun who would most likely be on ORB until he's needed for battle once more to act as Cagalli's sword when the ORB military has its hands tied or is needed to stay to defend ORB.
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