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:
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Two different Forms 1099-R are required because the coding in box 7 is different for these two distributions. The Form 1099-R for the offset distribution will include code M to indicate that you generally have until the due date of your tax return, including extensions, to come up with the money to roll over some or all of the offset distribution. However, if you qualify for these to be treated as coronavirus-related distributions and report them as such, you have 3 years to repay the distributions.