Originally Posted by SRD
Size and Type
Templates often change a creature’s type, and may change the creature’s size.
If a template changes the base creature’s type, the creature also acquires the augmented subtype unless the template description indicates otherwise. The augmented subtype is always paired with the creature’s original type. Unless a template indicates otherwise, the new creature has the traits of the new type but the features of the original type.
Your animal companion doesn't lose access to the animal-only buffs for becoming a magical beast, since it keeps the Augmented Animal subtype.
This probably applies to classes and prestige classes that change your type at some point as well (Incarnate, Monk, Green Spice Addict, Renegade Mastermaker, etc).