If your machine is homed correctly, the G53 should make it RAISE to the absolute Z zero (0). If it's going down, that means the machine (a) is not homed correctly, or (b) has lost position. For some reason, the machine thinks Z zero is down toward the table.
Make sure you've homed the machine before you start a part, then try re-homing it before running the restart.
Hope this helps,