You can. But I would not recommend it. (I assume this is a paper audit.) If your amendment doesn't agree "exactly" with any changes made by the IRS, then you're just inviting yet another audit. Now if this is in fact, a paper audit where you got something in the mail where the IRS is saying "this is what we changed", and you agree with it, then basically it's done. You can go ahead and amend your return to make it agree with what the IRS has already changed.
