Originally Posted by
Niwashi
There is a warning but it's not clear what it is that it's warning about.
It tells you that chocobos below rank 40 are lost if retired, but not that this chocobo you're trying to retire would be lost. The reason that's a problem is that, due to the confusion between rating and rank, people doing it think their chocobo is already above 40, so that that warning wouldn't apply to it.
If it instead said something like "Your chocobo isn't ranked high enough for breeding and will be lost if you retire him. Do you want to retire him anyway?" then it would be clear that you shouldn't select "Yes" unless you're trying to discard him.