Sorry for the late response. Its just busy this time of the year.
The answer to your question can be found in the instruction to Form 1040X.
Here is the link- read under purpose of the form-
It does not clearly state that you can file after or in audit. But it does say that it can be used to amend figures previously adjusted by IRS.
Also, in practical scenario- I have seen taxpayers amending the tax return. Also, you would not find any publication or regs that state that you cannot file amended tax return in audit. It only specifies that time period within which a tax return can be amended.
I will also refer you to a lawfirms website which talks about audit and your rights-
Let me know if you have any question.
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.