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Using Windows 10, QGIS latest version. Use Q chainage (vector plugin) to make a chain of points on a boundary (line vector layer). I save the points layer (as layer definition file), and also save the whole project. When I close and then return to the Project, the points are not there. The name of the layer is listed in the layers, but it is empty.

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You need to save the layer as a shapefile or similar. A layer definition file saves only the style in case you want to apply it to another layer later

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