In 2-player team leagues, often the format is match play where the "A" player plays against "A" and B plays against B. When a sub plays for one of the players, you can control how the sub is flighted in the match:
By default, the sub will play for the absent player regardless of the handicaps of the players involved
However, if you want the system to re-flight the matches when necessary, you can turn on setting #85 "Re-flight subs by handicap".
The downside of turning setting #85 on is that if you have a new sub without a handicap, you really don't know if the player is the "A" player or the "B" player. The printed scorecard will make the player the "A" player, but that may change after the fact once the score is entered and handicap calculated for the player.