In terms of your responsibility, in my personal opinion (which could be wrong)
If your job is bookkeeping, your job is only limited to record what happened. You do have an obligation to report or speak up your concerns about certain things, but you are not legally liable if no one listens. It then became a ethic or personal comfortability issue.
You are legally liable if you as the accountant, knowledgly misrepresented the financial position of a company, or committed a material mistake that caused financial and legal consequences. That usually comes with a certified statement, OR if you hold an important (managerial) position in the company (that potentially lead you to have benefit gains from the misinterpretation).
In the first position, there are ways to defend yourself in case it happened. In the second position, there are still ways but it usually doesn't work very well, so it might be better to find another office to avoid trouble.
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In terms of tax consequences, it will depends. If it's a C Corp and there's declared stock, then you ran into a dividend problem. If it's a partnership or LLC, less of a problem because it's usuay use a withdrawal and the tax consequences falls under the shareholders. (I might be wrong.)
If it is not a stock and dividend crap, then thr company's tax is right, because any withdrawal is an expense (any kind).
There's not enough information to determine if there's a tax escape, because we do not know what happened with the money. He could be paying someone as a contractor with 1099 MISC, or if he consider those as his shares of money, of if he wrote it as his payroll (which then he didn't pay payroll tax). If at the end of the day, someone paid taxes, then it might not be a problem.
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I am not an expert of tax. I'm reading it from a law perspective with the limited information.
New York - NYC
Passed CPA Exam (11/2014)
In search for a position in NYC that will fulfills the license requirement.