I quote:

"To update our records with the change of vehicle details, you must provide evidence from the list below (choose one)

1) A receipt of purchase on headed paper, from a garage, confirming the engine number, engine size (cc) and the fuel type for the reconditioned or replacement engine, if one has been fitted.

2) An inspection report from an organisation such as the RAC or AA.

3) An inspection report provided for insurance purposes.

4) Written confirmation from the manufacturer showing the engine number and size.

If your existing engine has been converted or the change took place before you bought the vehicle we will accept:

5) Written confirmation on headed paper from the garage that carried out the conversion;
OR
6) Written confirmation of the change on headed paper from an independent garage."

For the amateur mechanic carrying out an engine conversion or modification using second-hand parts, this looks like a big headache. However, in practice, if you are on good terms with a local garage that does your MOTs, I suspect that they will be willing to provide a letter "for insurance purposes" confirming  the identity of the engine, that the parts used are fit for purpose and that the work has been done to a good standard.

This procedure is apparently designed to combat the growing problem of high value cars being stolen and broken for parts that are then sold on the second-hand market. The Federation of British Historic Vehicle Clubs has already raised the issue with the DVLA and is working on our behalf to make the procedure more user-friendly for the amateur home mechanic and historic vehicle restorer.