Open the .pcb file with any text editor. It's just a text file. The project file is in there:
KEY ProjectFile "..\141190_A0.prj"
So you can read the file with your application into a list, modify it, and rewrite. This would require some method of knowing the correct project file, and perhaps closing and reopening the PCB with your application, but all that would not be very difficult to do.
Take note you also have to link the PCB to the project file. There is a way to set this on the DxDesigner side with ProjectData.SetPCBDesignPath. You may want to experiment with that and see if it also modifies the .pcb file.
Thank you very much, I didn't think it would be so simple...