So I finally had to use the Estop button. It worked fine. I powered down, reset the Estop, then powered up.
At this point, I would have wanted to manually drive the rails to clear the collision, but the only thing I was allowed to do was to home the machine. Not really the best action in some cases I suspect.
I would strongly suggest you take the user directly to the manual jog mode after an Estop so the user can tell the machine how to get out of collision.