This is a cut&paste from the USBC rulebook:
Rule 8 - Deadball
When a dead ball is called, the delivery does not count and the correct pins must be respotted. The player is allowed to rebowl that delivery.
A ball shall be declared dead if any of the following occur:
After a delivery, attention is immediately called to the fact that one or more pins were missing from the setup.
It would be MY assertion that, if it was only noticed AFTER the pins were reset for the second shot, and only because of the automatic scorer providing a score of 1, that the attention WAS NOT immediate and that he should've gotten 0 for that shot, but had the pins correct for his SECOND (spare) attempt.
Because of his lack of attention, and that of his team mates, the missing pin wasn't called in time, and the bowler in question should've been given the score of 09 for that frame instead of 9/.