Live Z-Adjust disappears around when the first layer finished printing. Josef Prusa explains it here ( for older Firmware revisions): https://www.reddit.com/r/3Dprinting/com ... 2/d655nkx/
Not sure how Pronterface influences things, i never used it. I don't think it is meant to do live changes to the nozzle position during a running print, but I could be wrong..
With respect to alternating z-offset for different materials: you could try Process Settings -> Gcode -> Global G-Code Offset -> Z, but changing it via the S3D interface it is profile and not material dependent.