This may be of help, but it does involve stopping the machine though.
I have individual 'axis enable' switches fitted to my control box. When making signs that are longer than the table I pause Mach, cut spindle power, disable the Y axis, release the work (vacuum table), manually wind the table to it's new position (leaving the work in the same position relative to the tool). Clamp work, apply spindle power, enable y axis, restart Mach. This sounds more complicated than it actually is to do but as Mach is unaware that any changes have been made it continues with the job just as if my table size was much larger.
In your case, I think, pausing Mach, disabling the z axis, winding it down to the required position, enabling the z axis and restarting Mach would work.