The main problem I have after this happens is making sure the right player is shown batting from that point forward. If I miss one, the stats will be wrong for two people. At a minimum, it would be helpful to have a toggle in the Game Settings: "Verify Each Batter" which, when enabled, would show me or prompt me to select the next batter with the expected batter shown as the default. Ideally, it would be great to also be able to temporarily insert a batter who may or may not already be somewhere else in the lineup. The next time around, the lineup would go back to normal. Of course, these changes would need to be implemented in a way that didn't create extra work or confusion when scoring normal games, but FTM's programmers are pretty good -- I know they can handle it.

A side question: how many times can a substitution be made in a batting position? I have seen 7 listed in a position in the scorebook for some of the games I've scored after all of the subbing.
For those who may not be aware (I wasn't until recently), this may seem like an unusual request for a small niche, but college showcase tournaments are pretty common and some are very large. I was told our next one may have 250 teams attending.