The plan administrator sending you a check for the remaining balance in your retirement plan, has the same implications as you taking a distribution from your retirement plan. Unless you rolled the funds over into another retirement plan within 60 days, the amount is taxable and (if you are under 59 1/2) subject to a 10% penalty. As for what you do, you enter the 1099-R, and the amount of the distribution will be included in your taxable income. If you rolled the money over, there will be interview questions to indicate so.
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