From the NCAA rulebook - Rule 4, Section 2, Article 2
Section 2. Alternating-Possession Procedure
Art. 2. The alternating-possession procedure starts when an official places the ball at the disposal of a player for a throw-in and ends when a passed ball touches or is legally touched by an inbounds player, when a player, who is located on the playing court, touches and causes the ball to be out of bounds or when the throw-in team commits a throw-in violation.
From the NCAA rulebook - Rule 6, Section 3, Article 4
Section 3. Alternating-Possession Situations
Art. 4. A foul by either team during an alternating-possession throw-in shall not cause the throw-in team to lose the alternating-possession arrow.
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So, how do you interpret that last one? I would say if the foul is on the inbounding team, then they lose that possession, but keep the arrow. If the foul is on the defending team, then the inbounding team keeps the arrow for that moment, but once it makes the inbounds pass, the arrow should switch.