| I am not very clear, did you mean to say the company corrected the 1099-Misc by amending the payment sent to you and instead showed a payment to your company?
Now, if there is an IRS inquiry, I would at that point hire a CPA to review your specific situation as it sounds quite complicated. There could be some valuation issues that may be involved in this case. I would recommend that you find a competent and experienced CPA to handle your case. | 
