Bevendre

Chaos is the natural order of things, and chaos magic is a reflection of this.  The magic of ponies and other sentients is Order magic, and acts against Chaos magic.  The magic of ponies and sentients has come to permeate Equestria to such a point that it suppresses Chaos magic like a dam does a river.  On some occasions, Chaos magic can leak or even burst out and alter the ordered world, creating new creatures or changing one thing into another.

Think of chaos magic bursts like a swamplight or ball lightning, a rare thing, but a natural thing.  It can’t be stopped or fully understood, but it’s nothing to raise a panic over (the effects are a different matter).  Furthermore, because it can change something into something else it has the potential of altering memory and to an extent reality as some perceive it, hence Papillon recognizing Libellule as her natural daughter.

As for Good Will the pony, there may be some problems that arise, but nothing that will cause great strife.  And no, Doctor, you’re not allowed to eat him.