Dash just informed " Key Fob Not Detected " then shortly after I lost all power?

I got some work done on my transmission and drove my car home just fine. The next morning it would not start. At first my dash just informed " Key Fob Not Detected " then shortly after I lost all power. I have tried new key fob batteries being careful not to touch with my hands and feel I have installed it correctly even going as far as using alcohol on Q-tip swab to clean the connections and the circuit board. I had a friend hook up jumper cables at the same time because I read that a key fob can drain a battery if left in the car when it is not running. Perhaps the mechanic did that or something got un-programmed when he was working on the transmission? But again, it started just fine, picking it up the night before. It did read the key fob briefly with cables hooked up, but the engine would not turn over. New key fob from the factory is $400.00 with programming. Ouch!
Could this be battery issue (battery is only 3 months old)
or does it sound like a bad key fob?