Q: Purchasing a car that, due to motor issues, everything was taken from another one and placed in that one.Potentially a problem car

I am looking at purchasing a car that was owned by a fleet company. They brought it to a repair shop with motor issues that were going to cost a couple of $1000 to replace. As they were deciding, they got into an accident with another of the same car. They decided to take the insurance money and sold the cars to the auto shop. The auto shop took everything out of the car from the accident and put it into the car with the motor issues. The only thing left of the original car was basically just the body. They say they've made all necessary repairs and there are no problems with the car. The carfax look good, it drives smoothly. The car now reflects the mileage of the other car as well. My next step was going to be to take it to another auto shop for a pre purchase inspection. But I am just wondering, could this potentially a problem car if the transplant (I guess) was not made correctly? The place I called for the inspection told me I should be very careful before purchasing this car.

My car has 46000 miles.
My car has an automatic transmission.