If you wish to combine two sets of edges then do that before calling geometryFromEdges. If you want to replace an existing geometry with a new one then delete the existing geometry first and then call geometryFromEdges. You can delete the existing geometry as follows:
pdem = createpde
g = @squareg
geometryFromEdges(pdem,g)
delete(pdem.Geometry)
pdem.Geometry = []
% Now you can call geometryFromEdges again
geometryFromEdges(pdem,g)
