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When I perform my mapping with TheSky6 + CCDSoft + TPoint + AutoMapper, all my shots are binned 2x2. There's certainly no problem with that.
If your query is around "mixed binning" ie, taking some mapping shots at 1x1 and others at 2x2 ... I am not 100% certain as I have not tried it but I don't see why this would have any impact providing the plate solve is correct in both cases (which relies on CCDSoft correctly plate solving the 2x2 or 1x1 image).
If you manually map (take a photograph, centre the star, then click map) then binning definitely has no impact - it's simply a case of you centering the star correctly before you map the additional point.
If you have more questions about TPoint I suggest you ask on the Software Bisque forums. You normally get a quick (24 hours) response fom Bisque to such queries.
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