Note: This lore comes from Pokémon Go but I'm asking the question here instead of Arqade Stack Exchange because I specifically want to know about the lore.
This says that the Shadow Effect that team Rocket puts on Pokémon makes them more powerful:
But once you free a Pokémon from team Rocket, you can purify them. According to this description, purifying the Pokémon makes it more powerful too:
This seems like a contradiction because purifying seems to imply that you're returning Pokémon to the way that they used to be.
Unless a Pokémon is ultimately better off after being turned into a Shadow version and then purified than if simply nothing had been done to it (which would be a counter-productive narrative since then we should actively try to turn Pokémon into Shadow versions so that we can purify them).