Your question is somewhat vague, but suggests that you converted some amount to a Roth IRA from a traditional IRA or from a traditional account in a qualified retirement plan. Converting an amount to Roth and then recharacterizing back to a traditional IRA does not create new nondeductible contributions in the traditional IRA. It only restores to the traditional IRA after-tax amounts that were in the traditional account prior to the conversion.
The recharacterization does not create after-tax money in your traditional IRAs that was not already after-tax money prior to the Roth conversion. By not filing an amended tax return before the 3-year statute of limitations for obtaining a refund of your taxes paid on the Roth conversion, you've simply lost the refund that you would have been entitled to receive had you filed the amendment in a timely fashion.
If some portion of the original Roth conversion was nontaxable due to coming from after-tax contributions to a traditional account in a qualified retirement plan or from nondeductible contributions in a traditional IRA, you must still file an amended tax return with a corrected Form 8606 even though doing so will not result in any tax refund due to the expired statute of limitations for obtaining the refund.
