Reference Waypoint

I was curious about having a calibration tool on the end of the robot. which I can align each time I move the robot to a new machine.
For example: If the robot is moved from machine A to B and then back to A if it doesn’t line up 100% correctly our programmer has to re program some points in order to produce parts. If I had a calibration tool on the end of the robot which fit into a mating part attached to the machine would it be able to reference this point and shift the program accordingly?

Yes, Take a look at what UR calls Features. They are reference points/lines/planes that you can teach your Waypoints against. Modifying the position of this Feature will shift all Waypoints accordingly.