If the SI's specified the inner/outer courses directly in conjunction with the respective color, as a sailor and as you did, I have to respect "intent"...clearly they didn't mean to send the monohulls around the longer course.

However, from a technical perspective, someone would need to protest the race committee. The race committee would really have no choice but to discard the races that were run with the marks in the wrong position since the SI's were in conflict with themselves due to a race committee error. I suspect that if someone protested another sailor on this issue, the result would also be that the race(s) would be completely discarded for everyone.