We've not heard of similar issues with the Preserve Ref Des option. When you say you make a change to a net name, where is this done in the DxDesigner Schematic or the Altium source? If the change is done in the source then I'm not surprised Ref Designatotors are different, the netlist wouldn't be associated with the original DxDesigner version translated earlier. If the issue is with changes made in DxDesigner then I'd suggest you log an SR with your support organisation.
all changes are made in DxDesigner. After translating the Altium schematic to DxDesigner first time, all schematic changes are done twice. One time in Altium only for documentation issues and the other time in DxDesigner which now is the "master schematic".
I will contact our German distributor to log on a SR