You should definitely go to a CPA who is experienced in tax matters and get this done! Having two different people doing your returns (one personal and one business) was your first mistake. I don't understand why you would have a schedule C if your business was run in your corporation. You do have the right to deduct your business expenses. You can keep disputing the IRS decision through 3 years after the due date of the original return. You may want to get to the Taxpayer Advocate. But, FIRST, go to an experienced, seasoned CPA firm and make sure that your tax returns are correct, once and for all. Then submit the final returns as amended returns and have the backup for all deductions ready to go for an examination.
Your first mistake was not going to a seasoned CPA in the first place.
Marty Davidoff, email@example.com, 732-274-1600. This answer is provided for general information only. You should seek advice from an attorney or tax professional.