FED does allow a team with nine players to have a substitute runner (not a courtesy runner) when a player is injured and cannot run the bases. The substitute must be the most recent batter not on base.
And, the injured player can return to the game if / when he has sufficiently recovered.
That sounds to me (perhaps) like what happened.
The cases are in rule 4 somewhere -- whatever rule deals with playing with 8 players.
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