As Nemezis said, it depends on how the battery and charger were wired.
If the battery was in parallel with the sound card and charger, then the soundcard probably saw that full 12v. Some boards are OK with that, some aren't.
If the charger disconnects or there is another way the battery is disconnected from the board, then it shouldn't be an issue.
There SHOULD be a disconnect. It is improper to leave the batter connected to the electronics while charging, because the draw from the electronics will create a risk of overcharging the batteries. If the batteries have a protection circuit (they SHOULD) then this isn't necessarily an issue, but it's not something you should rely on.