Yeh, there’s definitely something misleading about this story.
I am very familiar with the story.
The charge Rabbi Eisemann was convicted of was not the main charges they went after him for. In every newspaper, they said that he stole government money meant for the school. The jury cleared him of all those charges. The remaining charges were spoken about for only a minute or two during trial. They would've fallen off when the jury cleared him of the charges of stealing if not for the fact that the judge changed the rules last minute to make the charges not depend on each other (this happened after the defense finished presenting their witnesses.).
It is highly likely that the bookkeeper never knew that her entry had anything to do with the case, and being that she was one of three bookkeepers that worked for the school - and she doesn't anymore, it isn't strange that she was not involved until it became clear that Rabbi Eisemann is likely headed to prison.
If this is not clear, feel free to PM me.