on the v5 logbook there is section for entering changes i.e colour cubic capacity etc.
personally my car was registerd as a 1700cc and green.
i filled out the changes to blue and 1300cc and the engine number.
i recieved a new logbook with blue as colour and no engine change.
i refilled new logbook out with 1300c and engine number.
I then recieved a letter stating i needed supporting evidence.
this could be 1. donors logbook 2. engineers report 2. mot testing station letter of statement.
i had for mine the donors service book stamped by supplying dealer with engine number and cubic capacity as 1300cc.
my mate works in an mot station so he did me a letter on headed notepaper detailing he had inspected car and mot'd it and confirmed engine fitted and engine number.
I then got a logbook. and cheaper tax
took a while as dvla/vosa really slow.