Based on the letter from Paul, which specifies which players were in question for each of the 3 games, I believe the loss of stats is specific to those players only.

If you look at the NPF recap for August 2nd, Monica's line is all zeroes, and Kelly Kretschman was completely removed. (Kelly had a bunt single that game.) The same is true for July 13 and July 15. I know on the 15th that Germaine Fairchild had a pinch-hit single, but she does not appear on the recap either. You can also see that the total number of hits is greater than what appears in the box scores. The same is true for the 13th, as one of our hits appears to be missing, so Fairchild likely had a hit in this game. Further evidence of this is that the team stats now list Fairchild as having 3 hits on the year, and my copy of the stats before the game last night had her with 5.

If this is indeed the way the rule is written, at least it would mean that the rest of the players will get to keep the stats from that game, such as Oli's 3 HRs.