You already know the total rent received for a property for the tax year. Enter the 1099-MISC as printed. That will be less than the total rent actually received for any one property for the entire tax year. enter the 1099-MISC income in the rental income section specifically for 1099-MISC income. Then just enter the rest of the rent for the tax year in the section called "Other rental income not reported on a 1099-MISC or 1099-K" and press on. The total should add up to the total income received for that property for the tax year.
It flat out does not matter which rental property you assign the 1099-MISC too, as the IRS only receives the "bottom line total" and that's it.
