It is not unusual for horses to receive minor injuries on XC. Scratches, scrapes, bruises and pulls. Some can be foot sore. Some horses will pass the final vet check and jump stadium without risking further injury. Others may pass final check and jump for team placings then be withdrawn. Others are presented and are held for review, as in Boyd & Otis. In this case Boyd withdrew instead of representing, some are accepted on the 2nd check and some are spun (eliminated). For the record there is no recourse to the vet check decision.
My guess is the rules do not allow for subsitution between the two SJ rounds. The eligible 25 are set after the 1st round and that is it.