All command positions on a Yaskawa robot are stored in encoder pulse counts.
If you want to work in XYZ, you either have to use Position Variables in XYZ or use RELATIVE JOB (purchasable software option) to convert your positions from pulse to XYZ.
I apologise, I wrote incomplete. I am working on relative jobs to shift my user frames later, but relative jobs do not save the configuration part of the points. Is there any way to solve this, this is my main question?