As elevator mechanic (big or small companies), We repair elevator equipment everyday. I'm hopeful that "as mechanics" we make good choices. But I also so know that the mechanic is usually not consulted on which jobs to take or not take.
Dan Zeitz was kind enough to post "Jumpers--Mechanic goes to jail" in print talk. The article explains that the mechanic was charged and prosecuted for his actions while working on an elevator. The choice not to secure control of the elevator before bypassing any part of the safety circuit is a bad choice. Bypassing the entire safety circuit was in this example CATASTROPHIC!
So with every repair you may want to ask yourself, How far do you think a Lawer will go to point the finger of blame at the mechanic(s) who have worked on this elevator?
With all the information I have to form an opinion, It is my opinion that if the controller (as you claimed) completely went on fire, replace it. How much money could you have saved the customer? And like you said "the elevator runs almost perfect". If the customer is tight with their money, ALMOST PERFECT will haunt you for some time.
And if for some reason you find yourself in court! Don't forget to mention "the elevator was running ALMOST PERFECT"!