the dye cost 50 chocobux and will affect the chocobo registered to your Chocobo Whistle. As soon as you change or update the choco on your whistle though, the dye will go away, or as they say in-game, "wash off". I think if you have 0 charges, and renew a whistle, that the dye will not go away. The dye should remain, as long as you don't reregister the same choco to update stats, or change the choco, but I'm not sure, haven't tried it.