Why would the transmission not shift at 40MPH? I took the car down to the local shop and they said flushing it will probably kill the tranny. This problem has only occured once and the car seems to be ok now. Are we on borrowed time?
How many miles do you have on the odometer?
Was the trans fluid changed every 3 yrs/30k miles, whichever comes first?
If the trans fluid was not changed as per the above schedule, and if the odometer has over 90k miles, then trans failure may well be imminent. The best suggestion that I can give you is to take the vehicle to an independent trans shop (NOT AAMCO, Lee Myles, Cottman, Mr. Transmission, or any other chain operation) for an evaluation of the trans.
There could be any number of reasons for missing a shift. I would let a trans shop check it to be sure. Dont assume the worst, it could be something as simple as a sensor problem.