My girlfriend has a 2002 A6. She wore the rear brakes down real good to the point that the left rear caliper blew the piston out of the caliper. I got a new caliper and replaced the pads and rotors, but I dont get much if any pressure to the rear brakes now. Could it have screwed up the proportioning valve when the caliper blew out? I have bled the lines and am only getting fluid (no air) out of them, there is a ton of pressure when I bleed the fronts but it barely trickles out the back bleeders.
I don't know what is wrong with it.

There are pressure gauges on the market that you can screw into the bleeder valves. Then you can measure applied brake pressure and compare them to the service manual.

It sounds unlikely that the system was damaged at all. Perhaps you got some debris in the lines, and it's clogging the bleeder valve.