There;s no way to know what is going on without a lot more specific facts. You may want to take everything to a tax professional.
In general, anything your employer pays you as a result of your service for them should be considered taxable wages and reported on a W-2. "Settlements" are taxed according to what they represent. For example, I know of a small pizza chain that was forced by the state to pay back wages to their drivers, and pay them for the use of their personal cars. The part of the settlement for back wages were reported on a W-2 because they were in place of wages, and the payment for use of the personal car was taxable, but on a 1099-MISC, because it was not subject to social security and medicare tax, and because the employees might have taken mileage deductions (this was before 2018). A settlement would not be completely tax-free unless it was for a personal injury.
Then, I don't know why any settlement would be reported on a 1099-R, that's retirement income.
Let me try a guess, though. Suppose you were underpaid and due back wages. Suppose the under-payment of wages also resulted in under-payment of contributions to a 401k. So the employer needs to put some extra money into your 401k. But suppose you quit and closed out or rolled over the 401k to another account. In that case. the employer pays you directly, and since it is for retirement, it is on a 1099-R. (In that case, you would have 60 days to roll it over to an IRA to avoid tax.)
Out of curiosity, what is the code in box 7 of the 1099-R?
While you can add the 1099 to your return and then zero out the income with a correction, it would be better to get the employer to cancel the duplicate forms in the first place, if they are duplicate. But it's really unclear what is going on here. What is the basis of the payments and settlement ?
