Do the job, issue EIC and hope building inspector accepts it. To be fair when i have done similar, a rewire or part rewire and new extension they have always accepted my certs, and i have not needed to notify for the rewire, however i was an Elecsa member, and my certs had their logo on, so whether or not it made a difference i have no idea. If i were you i would do the job, issue the certs and see what happens, if you have to notify them of the rewire and pay the fees seperately, then that is what you will have to do. My gut feeling says you will be OK.
Cheers...........Howard