More I think the confuser I get! BOO, imp batter???

[SactoBlue]

Situation: Flex bats (shame on her) gets double.
#1 batter hits, gets single batting in Flex. #2 batter hits, get double driving in #1 batter. Defense now questions that Flex batted. My thinking, this isn't improper sub since she's in lineup already and she didn't bat for DP anyway. If it's BOO, once the 1st pitch to #2 batter occurs it's all over isn't it? Appeal was too late. The more I think about this the more I get confused...bottom line, I told'm it was too late and we went on but what is the situation and the logic to make this right?