I have it working quite well in testing here with a 56u PoKeys. I have the encoder output from a servo drive connected to the pokeys and can count the encoders into a DRO in Mach. I have some VB in the reset button and when I press the button it compares the machine coordinates with the encoder reading and if it is within 0.001mm it will just bring Mach out of reset. If however the encoders and machine coords differ by more than 0.001mm then a box will pop up asking if I wish to update the machine coords from the encoder values, if I click Yes then it will and then Mach will come out of reset. I have attached an image below of the box I was talking about, I also have the encoder and machine coords displayed in that message box so I can compre before I opt to update or not.
In your situation what you would need is an encoder fitted to the disabled axis and a pokeys 56U. What you would do is home the machine at start up and zero the encoder. You would then do whatever you need to do, disable the axis and use it manually then once finished press a button on screen and it would update the machine coords in relation to the encoder counts which would then update Mach as to the position of the axis after the manual motion.
Hood