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I had a player leave in the middle of the game. At the time, I thought I could just go into the line-up and mark him as not batting. It seemed to work throughout the rest of the game. Now when I go back and look at the detail, I see that it removed him from the game.. from the beginning. The activity and results of his at bats are there, but they are attributed to the wrong batter. So:
1) how should I handle a situation where a batter leaves the game?
2) how do I fix this for this game?

When a batter leaves a game and nobody has subbed for them, you would use Misc -> Skip Batter when there turn to bat comes up. If you remove a player from the starting lineup, then as you see, you are actually changing the starting lineup from the beginning of the game. You can edit the starting lineup again to put him back in the game (go to Game Manager, select the game, select Pitch by Pitch, tap the Game Starts even, and tap Edit next to Starting Lineup to change the starting lineup. This will likely mean the at bats after he left will be for the wrong players however. You can undo back to that point in the game and rescore from that point forward, or you can rescore the game (takes about 15 minutes to rescore a full game), or you can override the stats to get things the way you want. The following link shows what can be done with post game edits:

http://iscoresports.com/baseball/kb/faq ... _edits.php

It would be nice to have a checkbox on the "skip batter" option to indicate that the player should be skipped for the remainder of the game, so that you don't have to remember which player needs to get skipped. I had one the other day where two separate players left the game early and had to be skipped each time. Needless to say, I ended up having to re-score most of that game.

On Apple devices, once you have skipped a batter, iScore will ask you the next time through the lineup if you would like to skip them again. We will add this to Android versions in a future update as well.