Unfortunately - while you may amend your past returns - you generally would not be able to receive any additional refunds for some returns due to statute of limitation.
The statute of limitation to claim a refund is three years from the time the tax return was due.
Thus - for 2006 tax year - the tax return was due on Apr 15, 2007 and statute of limitation will run out on Apr 15. 2010.
So you will able to claim additional refund on 2006 and later years only.
Generally - if the business loss is claimed for more than two years - that might trigger (but not necessary will) an audit.
Please also be aware that the loss deduction resulted from the S-corporation is limited by shareholder's contributions plus loans provided to the S-corporation.
Let me know if you need any help.