@Schickfus I have not run into this issue but I remember another discussion about this on the forum in the past, can't find it right now.
Personally, if its an emergency and you hit the emergency stop, cutting power, then having the recover requiring rehoming would be acceptable in my view however that may not be the same in your case.
Once you have reconfigured the 1XDs you can send the positions of the axes using G92. the approach of using a trigger to indicate the estop has been pressed, and then either prompting the user to clear the fault and then reset the estop, then running through the reconfiguration of the 1XDs and restoring position should work.