You are right. Any time the official blows the whistle during live action, the play stops. All officials have blown the whistle and wished they hadn't (saw it happen with 2 seconds to play in a tie game in the NCAA tourney 3 years ago.) In the situation you described, play stops when the whistle is blown, since neither team had control at the time, possession is decided by the arrow, with the throw in coming from the spot nearest where the ball was when play was stopped. The basket by team A does not count.
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