Wrong.

How so? The DH is listed in the (9-player) batting order. The player for whom he is batting isn't. Only one of those two can play offense at the same time, or play defense at the same time.

However, switching them isn't considered a substitution.

I never said they were switched for each other. Quite the contrary.

Not exactly the OP, but from the most recent NCAA Interps:

1. Code of Ethics, p. 10: Refer to items 1, 2, and 3. What is the procedure the umpires should follow when it is discovered that two players have switched base running positions during a
defensive time-out? Prior to the next pitch, play or if any member of the umpiring crew remains in the confines of the field of play:

Call any player out who may have scored:
a. Eject both players and the head coach
b. Administer Rule 5-15b, levy a two game suspension of the head coach for the
unsportsmanlike act.
c. Allow the conference to determine additional penalties against the head coach.

I'm not sure what the NCAA means by this.

I'm guessing they mean if the umpires don't catch the switch prior to the ball being put in play and one of the switched runners subsequently scores.

But it's preceded by the "prior to the next pitch or play" stuff. That's what's baffling.

Maybe that means "prior to the next pitch or play after discovery."

That could lead to an interesting strategy: Have F1 intentionally balk enough times to score all the runners, then 'discover' the error. But I am probably missing something. It wouldn't be the first time.

A balk is a play. Refer to interps and approved rulings on balks.