When I got the transplant from 1.3petty to 1.7D in the Jeep, I told the DVLA and insurers of the change. The DVLA later tracked me down and charged me extra for the tax I bought just before the conversion. If you didn't tell the DVLA, then got the car mot'd and went to get it taxed, you'd still get charged for the newer engine as that's what it'd say on the mot certificate. I'm sure the DVLA would track you down from this.
You'd need a letter from an independant garage who had nothing to do with the conversion saying that the job's a goodun too, for the DVLA.
Hope this helps