We don't know any more about your situation than what little you tell us, if you are working with an accountant, stick with them.
In general, if the IRS sends a letter proposing that you owe more tax for some reason, and you disagree, you would respond with a letter outlining your argument, and including any other proof or tax forms that support your argument. If the IRS accepts your argument, they would send a letter saying the case is closed. If they reject your argument, they would send a letter denying your claim and re-stating the tax you owe. That's the point where you would either appeal to their supervisor or take it to court.
It sounds like you have sent your letter and are waiting for a response, so you just have to keep waiting. The IRS is backlogged and not terribly competent even on a good day.
