If the IRS determines that fraud exists, fraud penalties could be applied to the additional tax accessed.
The fraud penalty is an additional tax of 75% of the portion of the underpayment attributable to the fraud. Filing 941-X or 94-X will not necessarily alleviate the penalties; however, this action would be a positive step should the IRS pursue a fraud penalty.
The IRS can and will be punitive in cases of fraud, so tread lightly and do what is correct and proper.