If the dealer didn't use a pressure system designed to "properly" flush fluid and used the old fashion method instead (one guy pushing the brake pedal the other guy opening the bleeders) damage to the m-cyl is "probable". When extending the piston in the m-cyl beyond it's normal sweep (normal sweep = top of pedal to position where vehicle comes to a stop - typically 3/8 to 1/2 distance from top of pedal to the floor) and going full to the floor board when bleeding, the piston extends within the cylinder to an area it never goes to normally, this can score the piston/cylinder, or damage the piston seals. Typically when this type damage occurs the brakes don't work as well or not at all. To me it sounds like something in the system failed and caused a "check valve" (one way flow only) to be created, therefore not allowing pressure created when applying the brakes to be released when not being used. Usually this is related to an internally failed brake hose = a portion of the inner rubber becomes partially detached, creating a flap that allows fluid flow into the caliper - but not out of the caliper. This situation will keep a constant pressure, or drag, on the brakes. One of the first things I did when I purchased my 99 (in 01 w/75k) was to change all brakes and hoses - the rear hose was no problem locating but the front ones were difficult and I was only able to find at a dealer. For some reason the local parts house only stocked hoses for all wheel anti-lock brakes = the front hoses for the rear only anti-lock were very different.
I can't imagine a "dealer shop" not having / using the correct tool to do such a job - sooooo much easier/faster = cost efficient than the old fashion method. However, it comes down to the Tech doing the job.
I'm not sure if your 01 has rear disk or drum, I think rear disk on 01s only came if it had all wheel anti-lock, or were ordered as an option, not totally sure? Either way, I'd check the rear pad/shoes too. If you find the front and or the rears are glazed and the rotors/drums show signs of being heated, you should be having a conversation with the Service Department Manager about corrective action being taken, at no cost to you, immediately. If you face resistance you can suggest to him/her that you belong to a membership of over 35,000 supporting members owning "specifically" Dodge Trucks w/Cummins power-plants and you've posted your problem on the membership website for-which everyone is awaiting to see if the dealership handles your concerns appropriately. Never hurts to have friends.
If you check your brake pads/shoes rotors/drums and all is well you can mark this visit to the dealer as experience and rest easy.
It sounds like they recognize they screwed up somewhere, they changed the m-cyl at no charge, but it's a little disappointing they chose not to check to make sure the pads/shoes were "safe" for you to continue use.
Keep us posted - if you don't have good results with the dealer you may wish to post the city, state and their name so as to warn other members of their service tactics/practices.
Attention: TDR Forum Junkies 
), I drove home 60 miles on the freeway and found both front brakes smoking hot -literally. Truck was trailered back to dealer who reported "seized master cylinder" and replaced at N/C . Is this possibly a coincidence or is it a botched repair job? Dealer did not want to replace pads. What would the signs be that pads got too hot for too long (60 miles!) and should be replaced? Don't want to find out the hard way.
