Transmission

The only time changing the transmission fluid will cause a problem, is if the fluid is burnt and thick. The seals are usually worn and when you put new thin fluid back in, it will leak past the seals and you will lose all engagement of your transmission.

Your problem sounds like an electrical problem, usually the Solenoid pack has a short in one of the solenoids and will set a code in the computer. The computer will automatically default to limp mode, which disables lock up and increases line pressure. Resulting in the hard shift you feel.

If they fixed your problem and changed your fluid and you drove it out of there parking lot without any problems, chances are you shouldn't see anything else til your up around the 200K mark. That's when the defects in the E40D start giving problems.
Hope this helps!