The problem has been partially solved because.
I have solved the disappearance of the BFD2 64bit plugin in the Instrument Browser Window. I did a reinstall of a BFD2 update, checking they went into the correct folders. After the reinstall the BFD2 64bit plugin was in the Instrument Browser Window.
But the project that would not load with BFD2 correctly, still does not load with BFD2 correctly. The project when loading would again inform me that Sonar could not find the CLSID for BFD2 64Bit VST:-
{141AC902-0000-0000-4246-443200000000}
So why did BFD2 CLSID suddenly change?, was it installing Sonar X3?c, or a problem I had with a Waves upgrade?, or both?.