Not if you can help it. The danger in filing is that the new return is fair game for the auditor, and she may get permission from her manager to expand the audit to include that return.
Instead of filing, file for an automatic extension until August 15. To do this, get IRS Form 4868, Application for Automatic Extension of Time, and send it to the IRS by April 15. But be sure to pay all taxes due on April 15. If the audit is still going on in August, request a second extension by filing IRS Form 2688, Application for Additional Extension of Time, by August 15. If the second extension is granted, you will have until October 15 to file your return.
If the audit is still alive on October 15, don't file until the audit is completed. As long as you have paid all the taxes due and have no fraudulent intent, you won't incur any penalties or interest for not meeting the deadline. If you owe additional money, send in your payment with a letter stating that the payment is to be applied to the unfiled tax year. The auditor can't make you file your return; if she asks you about it, simply say, "I am not yet ready to file."
For more on filing a late return and facing an IRS audit, see Stand Up to the IRS, by tax attorney Frederick Daily (Nolo).