Income Averaging is a method of computing personal income tax "whereby tax is figured on the average of the total of current year's income and that of the three preceding years. According to 1984 U.S. Tax legislation, income averaging was used when a person's income for the current year exceeded 140% of the average taxable income in the preceding three years." Unfortunately, the Tax Reform Act of 1986 repealed income averaging!
But, I would file your 2009 S Corporation Tax Return and claim all of your allowable deductions which would result in a loss as per your note. Now, these losses would flow to your personal tax return via the K-1. The result of these losses flowing to your personal tax return may be that you would have a Net Operating Loss in 2009!
Per Pursuant to Rev. Proc. 2009-52, you may elect "to apply IRC Section 172(b)(1)(H), electing a 5-year carryback period with respect to the net operating loss incurred for the tax year ended 12/31/09. Thus, you can offset the losses in 2009 against your potential income that you reported as far back as 5 years and obtain a tentative tax refund using Form 1045!
But, you must not be a TARP recipient nor, in 2008 or 2009, or was an affiliate of a TARP recipient.