Let's assume a lvl 9 druid casts Awaken on its Animal Companion. As explained by rules :
Most pointedly, awakened animals can no longer serve as companions, and the character must follow the rules for Leadership if he wishes to take the animal as an official cohort.
However, rules doesn't seem to clearly explain how the animal NPC should be created, apart from the direct awakening effects:
The moment the spell takes effect, an animal companion ceases to be a class feature, and instead becomes a person—an NPC whose Intelligence has increased by 3d6 (potentially making it as smart as or smarter than the caster), and who has an increased Charisma score and knows at least one spoken language.
I found several discussions on the subject. They all agree on the fact that the way it should be handled depends on the GM, however they don't agree on the "best" way to do it, for both balance and roleplay aspects.
Two main solutions emerges from my researches:
The first one involves to completely rebuild the Animal Companion from lvl 1 with class levels, involving that everything based on the link between the Animal Companion and the druid, bonuses, size, etc. suddenly disappears. It probably is the simpliest way to do it, but seems quite strange in my opininon.
The second, based on James Jacobs statement, keeps all the Animal Companion bonuses as feats, size, natural armor and STR/DEX bonuses, except special ones as Link, Share Spell etc. It then assumes it is a NPC with a level corresponding to its current number of Hit Dices. This solution seems more suitable for the roleplay part, but involved some disagreements about the balance aspect.
My issue here is based both on the balance and roleplay aspects, with priority given to the balance. I don't want the awakening to create an overpowered Cohort which would give the PC too much advantages.
Mainly based on the balance aspect, which way to handle this situation would result in an acceptable NPC for a Cohort ?
The solution doesn't need to be one of both I mentioned above. I just presented them to illustrate the issue.