It looks like you're new here. If you want to get involved, click one of these buttons!
Currently the method I know of writing a GDSII file is File -> Save As -> GDSII. But this produces a GDSII file that I can not trace nets in. I have tried tracing nets in other GDSII files and it works flawlessly.
Comments
@nofal That is weird. There are no specific flavours of GDS you cannot trace. Did you check the layer numbers? DEF may produce different layer numbers than you're used to.
Matthias