Mitsubishi Repair Problems? Ask a Mechanic for Answers ASAP
There are two things to note in this situation:
1) If water gets inside the transmission, the friction discs used for the clutches and brakes will deteriorate very quickly. They have a paper-like construction and the water will cause them to basically fall apart, as if they had been burned up from long term use. This will happen pretty quickly... within a few dozen miles it will usually result in failure, though if it is removed immediately you can sometimes avoid internal work. It is far from a guarantee though, especially in the long term. The act of flushing after a water issue occurred could theoretically accelerate the failure.
2) If the vehicle goes into transmission fail safe the N light will flash and you will have Park, Reverse, Neutral and 3rd gear. Whether you put the shifter in Drive or Low, you still will have 3rd gear. This is the computers way of protecting the transmission from causing any further damage in the event that whatever it saw "wrong" was capable of causing damage.
So with all that said.... While it is unlikely it was anything they did wrong (though very likely was a result of the flush), the fault codes placing it in fail safe would certainly go a long way toward indicating one way or the other what happened, so finding out what faults are set should be a priority before making any judgment on what happened between when you left the vehicle and when you picked it up.
It looks like we missed each other and I am heading out for the night. If you would like to discuss this further just reply back here and I will get with you upon my return.