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In NCAA, during a BOO appeal, do the outs made by runners other than the improper batter stand?

For example, 1 out, R1 and R3. In the top half on an inning, an improper batter drives one to the gap. R3 scores, R1 is thrown out at the plate (2 outs), and BR is thrown out at 3rd trying to stretch it into a triple (3 outs - inninng over). Teams change sides.

Now, in the bottom half of the inning, before the next pitch to the next batter, the Offensive Coach (formerly the Defensive Coach of the top half inning) appeals the batting out of order in the top half by the improper batter. The appeal is upheld, and so as a result, the improper batter and R3's run are erased and the proper batter is declared out; BUT what happens to R2and his out at home?

I'm trying to find out in the NCAA 2010 rule book whether outs made during a boo stand (as in the FED Rule Book).