Yes, always worth checking that your donor V5 and your engine have the same number!
There is nothing to stop you changing the engine number on your V5 while the car is SORN'd.
When you register a donor in your name you have the opportunity to change any vehicle details.
Lets face it that's a good time to change the engine number. It never actually has to physically go in the car does it?!
For instance what would the possibility of buying a late 70' or early 80's GTV and putting a 166 or 156 engine number on the logbook. Who would check it? So you can have an authenticly aged plate (not quite, I'll admit) and a modern engine/box.