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Having a points shapefile with z values, how do I keep in the geometry only the x,y values? I also want to move the z values to a newly created double field.

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What about exporting with appended Lat/Lon (Vector -> Geometry-Tools -> Export/Append Geometry Columns), saving as new file ? If the function is implemented 3D (sorry, I've no idea if) this should give you the required result. To make shure the z is dropped, you might export the result as CSV, edit and again load as new layer.

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I used http://converter.mygeodata.eu/ there I can convert a shape file to csv file with xyz or xy values. Edit and again load as new layer.

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