I'm glad they fixed the problem. I have a question though. Are you sure that the master cylinder wasn't leaking into the booster? A master cylinder can leak, but it would loose fluid externally and internally. A seal in the master can go bad and cause a sinking pedal, but not a loss of fluid. The only way to loose fluid like you said is to have an external leak.
You said that they told you the master cylinder is putting pressure on the calipers and this may have damaged them. This is how a caliper works, This could damage pads and rotors but not the calipers. Maybe you just misunderstood what they were saying, or they are wrong. I would ask for more information.