Presumably you are using the reg number that came with the diesel shell.
If not, you are a very illegal ringer and will probably be taken off in the middle of the night, never to be heard from again.

Assuming you are using the correct numbers, why not just record a change of engine number and fuel type?

To go about it entirely correctly would mean an SVA and with parts from two used cars you will probably get a Q (if they still do them?) or be unable to register the car at all.