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1) I rename the "C:\Users\ATEMVEGETA\AppData\Roaming\.minecraft\database" to "C:\Users\ATEMVEGETA\AppData\Roaming\.minecraft\customdatabase"
2) I add the converted files of H2 to "C:\Users\ATEMVEGETA\AppData\Roaming\.minecraft\customdatabase" and replace the old ones (the original ones)
3) Then I open Pixelmon and it should use the converted files instead?
By the way, Pixelmon modders seriously please fix the Air Persistent Legendary Pokemon in the next update. It's not just a minor problem, it's like they don't even exist in Pixelmon the way the spawn now. I hope I can actually catch them sometime if this gets fixed with an official mod and not an edited one. Thanks!