I don't know much about cries, because I never changed them, but I think if you wanna change the old cries for the new ones just take a free offset of your ROM, and with shappy introduce the cry, then if you go to PGE you will see that in the option cries the most subdued in which each cry is found, it would be enough to change them where it has its new displacement.
If I remember correctly, there was a problem with the offsets for the Pokémon Gen III, but I don't remember, sorry.