Let the auditor know you are in the process of amending your return. They may allow you to do that. But, it is not going to necessarily stop the audit.
It is not too late to file an amended return for 2006, but it will not necessaily stop the audit.
The auditor will give you full tax treatment, that is you could end up payin penalties and interest, as you would anyway on an amended return, or you could end up getting a refund. (I do not know which is the case for you because I do not know your tax situation).
Unfortunately there is nothing that will stop an audit once you have been identified unless you invoke the assisstance of a tax attorney he files legal documents with the tax court to get a temporary injunction.
Unless the IRS detemines for some reason after discussing with you and reviewing your amended return that one is no longer necessary. But, I can not tell you that it will be avoided. This is because something like that is completely discretionary.
So when you ask that question, I have to respond by what is availble in the code.