Fluke is 100% right.
There are different ways to make the calibration, but when you calibrate one axis the reference point for the axis can change. Always depending on the methodology used, but even with the calibration tool from KUKA it can change.
Robots use single turn resolvers to know the inclination of each of their axes and a lap counter to know how many turns each axis have done.
When you calibrate one axis you are telling the robot that the calibration position it's the new home for that axis, therefore you are affecting all the programs. OF course it can happen that you can't appreciate the change as the previous calibration and the new one would be identical, but this is only one possibility. Given your explanations, you've remastered one axis and now the programs are not ok anymore. You can do several things:
- Recalibrate the axis until everything goes back to normal.
- Use an advanced mathematical software to recalculate all your points.
- Re-touch-up all the points in the old programs.
Last two options only if you are certain that your new calibration is better than the old one.
To calibrate the robot axis you should definitely use the KUKA specific device.
Good luck!