flex bats

[cloverdale]

jv working alone...3rd out and coach comes to me and says the flex player just batted...I thought that the flex could bat for the dp but then you would lose the flex...so this is how i handled it...we let the books show that the lead off was out and started the next inning with the 2 batter on lead off...right or wrong it got the batting order straighened out...was this not only batting out of order but also an illegal subsitution...should I have sent the batter and coach to the dugout...what else am i missing on this play...how should it have been handled...now for a twist...if they would have caught this before the out what else would have changed?