[FrankJ]

Your proposal is not inherently against the rules.

My understanding is the disable just disables the outputs. The program in the crio is still running. So you can have code that monitors the encoders, you just have to stick it the right place so it runs during disable. You could input the start point from the smart dashboard. You can even put a push button on one of the inputs on the robot to mark the zero point of where you start reading your encoders from. Nothing in G05 prevents this.

The only issue would be G07 if you take too much time. A little practice would prevent this.