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Update, I just happened to come across it going around the map. It was roaming, but without the pokedex I was just flying blind. Took me around like 5-10 min of searching
I’m also having this problem, but I already had the second encounter with Raikou when you approach Moomoo Farm. It’s not in my Pokedex and I have no idea where it’s roaming, so I just can’t do the braille puzzle in the Ruins of Alph. Would also like some help if anyone knows