For at least my focuser, and likely many others, the "position" that's tracked really means the position of the stepper motor that turns the mechanical focuser. It does not mean the position of the mechanical focuser. (I suppose it's possible to keep track of that with optical sensors etc, but that's likely not being done.) So, if you detach the clutch and manually turn the mechanical focuser, I believe you are right that INDI/Ekos and the focuser controller itself lose track of the mechanical focuser position. However, if you use a focuser controller's user interface to step the focuser, then I would hope that the focuser controller (and INDI/Ekos) could keep track.

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