Oh Boy! we have a mess!

[udbomber]

If you had a count on as a referee, that is definite knowledge of how much time to take off.

If you ever have a count on and the clock does not match your count, you cannot adjust the clock to the violation at hand. For example, if the ball is taken out of bounds on a full court press with 15 seconds remaining and you whistled a 10 second backcourt violation with 2 seconds now remaining on the clock, you cannot reset the clock to 5 seconds to match the stopped clock with the 10 second violation.

Your count is the definite knowledge you have to go by so in the scenario posted, you could take off 2 seconds from the closely guarded count. It was a merited free throw so it stands and there was no erroneous information from the official so you now replace the disqualified player with B running the baseline for a throw-in.
I love this game.
Alan