I have a electrical fault on my 2.0 renault megane coupe 99 model?

I have a late 99 megane coupe with a possible immobilser problem. I had a key fob issue which i belive has not got worse. i unlocked the car with the key fob as per usual went away to put something in the house an the central locking system auto re-armed i,ve tried endlessly pressing the fob all around the car to see if it would pick up no joy. I had an alarm issue with another car an called the same guy out to dis arm the alarm as i found out it was a sigma aftermarket alarm. he took out the alarm but now the little led in the dash board has gone i can hear the fuel pump when you turn the key but the car will not start there is also what looks like the engine management light which is flashing every time yu try to start. Any advice on what we may have done and whats the best way round this?