Car stops working then works again 1-2 hours later
 

I own a 2006 Honda Civic Hybrid. The Vehicle has about 100,000 miles on it. Just hit that mark. The vehicle started having problems about 3 months ago. The vehicle would start but the IBA, Brake System and Check Engine lights would come on and you couldn't shift the vehicle out of Park into drive. If you do bypass the locking mechanism and force the car into drive (or neutral) the vehicle will die. After about 1-2 hours (depending on the day) the vehicle will function properly, and all the lights except the check engine light will go away. The check engine light will turn off a week or so later. This has been going on for several months. The vehicle tends to malfunction after not being driven for a while. The vehicle has been to two different Honda Dealerships and a mechanic known as Car Nerds who work exclusively with Hybrids. The vehicle had a battery replaced and that's when the problems started happening. The car nerds replaced the battery again and all it did was allow you to drive the vehicle when it was malfunctioning very slowly and not for very long. The vehicle could gain speed but only if you were driving it without interruption (without stopping) for a long distance. This eventually was not possible and the vehicle went back to malfunctioning the way it was before. Nobody can tell me what's wrong with the car. It's costing a lot of money to take it back every time this happens. They tell me the Hybrid battery is fine. Thoughts?