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The change in focal length is only going to be very slight as a percentage. We're just not sure how FC knows what your focal length is & particularly how it could know it has changed due to focus. We can't help you with WinJupos at the moment as our WinJupos is "broken" at the moment. All of our computers run Linux so WinJupos has to run under WINE and since the last upgrade, it has stopped working. From memory though, it would seem reasonable that the magnification of the planet has to be the same as you don't apply the measurement tool to every video.
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