I have for example 5 connections to AGND, and 100 to DGND. On the schematic I have one single trace that connects AGND to DGND to indicate that they are to have separate planes.
When I import the netlist in to pcbnew DGND is gone and all grounds are called AGND. How can I giver preference to DGND? or force it to ignore and not use AGND?.
To keep the individual identity of the two nets you have to join them with a component [jumper, 0-ohm resistor, net-tie…]. Then create a footprint that suits your needs best, with the two pads connected, to physically join the nets where convenient [e.g. star GND…].