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As far as I know all the software does is record the errors required to autoguide the scope. So if you select the correct mount now it should simply recalculate the correct period for the worm and adjust the graph as it at the moment thinks the worm is repeating its cycle when it is not and the resulting PE curve would be useless.
One tip also. I use Precision PEC by Bisque but it is similar to Pempro. Once you've done a PE curve, use it and watch the guide errors. If they are not better then your curve is off somehow. Most likely it is upside down like mine was - (took me 2-3 months to detect that!).
Greg.
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