Hey Peter,
A closed-loop stepper system does not mean that the machine “knows” where the carriages are. In fact it does not. A closed-loop stepper just means that with its glass disc encoder it compares the steps received with the rotation made, and if it deviates too much, it signals an error to the CNC controller which then can stop the g-code program. That is the difference to an open-loop stepper system where such a deviation is not sensed so the program is not stopped.
Also neither a system with closed-loop steppers can be aware of motor moves while it was powered off, nor a open-loop system can. What you want is always an accurate method of homing after power on. I think the photoelectric limit sensors should be such a system, but I have no experience with the Elite Series. I tend to consider inductive proximity sensors as the best regarding homing repetability. Because photoelectric sensors like on the Elite can be fooled by dust. If the homing repeatibility is perfect, and the error persists, there must be something that changed the position of the carriage or of the bit. But I don’t know how accurate the photolectric homing repeatability on the Elite is. However no amount of steps deviation are signaled to the CNC controller, not even the steps themselves are known to the CNC controller. It just sends steps and with closed-loop, it is able to receive an error signal from the stepper on its motor alarm wire, nothing more.
I have no experience with the jump to line feature, but there are a lot of modal g-code commands. Even the motion commands like G0 and G1 are modal, so when jumping to a line in the middle of a g-code program, not only I would make sure that the modal commands in the g-code preamble are all active, I would also make sure that the last modal commands before the line are active.