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My understanding and experience is the motors are only active during a print, they are disabled after the print is complete. At the end of the GCODE there will likely be an M84 command which is the command to disable idle hold. It could also be an M18 which just disables all stepper drivers. You could delete that from the GCODE if you don’t want it to turn them off after a print.
Sending an M17 should enable all stepper motors, so you could send that before setting the tool position.
I believe however that if you need to manually move one or both of the axis to get it square there is an underlying issue somewhere else. That might just be mine though, as I pulled the middle carriage apart on mine and noted the middle joiner pieces weren’t square to each other so I suspect there may have been a printing flaw when I printed mine.
Hope that information helps!