Could you change the class-changing seeds (Chaos seed, life seed, etc) so that, during breeding, the offspring maintains its class if the primary parent is the creature, and if the result is the same species (the same way Singulars maintain their status as Singular). Either that, or refund the seeds of any creature that is bred. By my measure seeds of a particular class are nearly as rare as Singular creatures, so I don’t want to waste their effects!
That’s a good idea. Maybe the interface currently used for equipment could allow you to select your default class or any seeded class from a parent.