Oh boy. Alright, so company A should have accepted your claim if there's a police report indicating that you were not at fault. Since A was the proximate cause of the accident he should be paying for your car. It is up to company A to subrogate against company B for whatever amount of the claim they believe B is responsible for. Your insurance company will return your deductible once they subrogate. However, this is something insurance companies do to avoid paying the full cost. They'll have you go through your own insurance and then they'll pay what they feel like at the end. It's rarely the full amount.

Regardless, yes you will get your deductible back. As far as diminished value, you have to be indemnified. So if it's a total loss they have to pay you for the vehicle's current value. If it isn't, they have to repair all of the damage from the accident. That's up to the adjuster to determine though.