No, the R134a conversion wouldn't have any effect on the vacuum lines.
If both valves are working, I would ditch one of them.
At the firewall, behind the engine there should be a rubber grommet with three vacuum lines coming out of it. One big and two smaller ones. The big one should go to a small metal vacuum reservoir mounted on the driver's side splash pan, this is where the A/C pulls its vacuum from. The two smaller lines go to the water valve in the heater hose. I forget which goes where and I'm 1600 miles from my tech manuals so I can't look it up right now. I "think" the black w/ red stripe goes to the fitting on the end of the valve and the black w/ green goes to the other one.