Not true: the system is set up to take you highest possible item in a slot into account when calculating the level of powerful gear, even if the item is in your vault. As long as the current item you are using being underleveled isn't holding you back, you can simply vault the higher piece of gear, and still get the benefit on your next prime or powerful reward.
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Lol I've still gotten a 542 edge transit while having a 543 rocket equipped from a prime engram
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It doesn't base off of the slot, it bases off the highest total average. So yeah, that can happen.