This is one of those situations where, if there is no material difference in tax, the best choice may be to let sleeping dogs lie. Amending your 2015 return and filing a delinquent 1120-S are going to cause both you and the IRS more trouble than it is worth, especially if there is no material amount of tax due.
Also if there will be any IRS penalties or fee, will my old CPA be held responsible?
You are responsible for any penalties on your return as presumably you knew that the Schedule C was incorrect and you filed the return anyway. However, if the CPA knew of the S-Corporation, most would correct their mistake at no additional cost to you.
