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So I'm mass cloning Unowns in Gold that hold rare candies so I can farm them and skip a lot of the stupid fucking level grinding for dex completion, like Tyranitar's absurd timesink, and my count is at like ~180 rare candies by now, but I still feel like it's not enough. So I did a test. I saved the game, fed a rare candy to an Unown to raise it to level 6, then cloned it. When I turned the game back on, I was at 180 rare candies again, not 179, the Unown in my party was level 5, and the one I deposited was level 6.
This means that one can skip the grinding and use infinite rare candies through incremental cloning. Additionally, this means that the Pokemon in your party is the clone and not the one deposited, because the one deposited is the true record of what happened, while the one in your party is a temporal clone drawn from a previous instance. So I can get a Larvitar to Tyranitar without spending a single rare candy.