There should not be a problem moving a SmartScope to it's extreme end of travel if you did it by joystick - so I dont know why you would be warned not to. It has pre and regular limit switches to ensure safe end of travel motion. Unless the PCDMIS retrofit removes that safety capability... if that is the case...
*** TURN THE POWER OFF ***
With the Z axis over-traveled you will need to get to the drive screw and manually turn the screw to move the axis.
*** TURN THE POWER OFF ***
Oh yeah, did I mention - *** TURN THE POWER OFF *** by unplugging the machine before removing any covers.
I have an older smartscope & have had folks who have done this. What I've had to do is take the cover which covers the drive belts & move them by hand enough to get the scope moving again.....HTH