Yes, you should receive a second 1099R.You will need to report both.
It sounds like you had taken a loan out against your 401k. When you later closed the 401k account, you should have had the option of repaying the loan, or having the account reduced by the outstanding loan amount. It sounds like you took the option of having the loan offset and receive a lesser amount.
The 10% penalty tax on that final withdrawal COULD be waived because of the CARES Act (if applicable). The TurboTax software will ask you about that. Below is a link to a TurboTax article with more information:
2020 Stimulus: Tax Relief for This Year's Taxes
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