Accuracy Related Penalty

If client / taxpayer who is currently under exam for year 1 and files an amended tax return (increasing taxable income) for year 2 prior to the agent actually opening the subsequent year for audit (which they did), should the subsequent year be subject to accuracy related penalties (assuming all under reported income was corrected on the amended return)?

See Reg. 1.6664-2(c)(2), (3) and (4).

Thank you!