What will happen if I overpaid the taxes on the extension form, but failed to file before Oct 15 deadline ?
Do I lose any of the refund ?
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You will not lose any of your refund as long as you file within 3 years of the date that your return is due. From the IRS website:
In most cases, an original return claiming a refund must be filed within three years of its due date for the IRS to issue a refund.
Generally, after the three-year window closes, the IRS can neither send a refund for the specific tax year. nor apply any credits, including overpayments of estimated or withholding taxes, to other tax years that are underpaid.