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According to the site at Homeowners refund
"Returns can be filed up to a year after the due date. After that, you cannot claim a refund. The deadline for the 2009 return is August 15, 2011."
To apply for either the regular property tax refund or the special property tax refund use Form M1PR, Minnesota Property Tax Refund.
Based on that information there should not be any problem in you still getting a Minnesota property tax refund for 2009 if you qualify.