I had similar situations before on RTWs. So for example ticketed AAA-BBB, but then changed flight times and there was no AAA-BBB. Only AAA-CCC and CCC-BBB as a connection which i booked.
In all cases they just took my AAA-CCC coupon, issued two boarding passes and issued a handwritten extra coupon.
Never exeeded the max. miles (to my knowledge), but i dont remember anybody checking. Ticket was allways issued as First Class open.