That's about it, at least if I was your certifier. If you do a good job of explaining, the certifier should understand. If they don't understand, a bit of back-and-forth may be needed.
Each segment should be measured as if it was a separate race course (shorter measured length etc). The segments, plus or minus a final adjustment, should add up to the certified length.
It's pretty much the same as if the course was measured on three or four separate days, except the days could be separated by a year or more.