Continue in the fashion that your accountant was using, i.e., you have two separate properties reported on Schedule E. They will continue to be combined for reporting purposes. (I assume your reference to "ACTUAL 1048, LINE 17" is referring to Form 1040, line 17 of the versions of Form 1040 used prior to tax year 2018.)
If your real question is "how do I enter one 1099-MISC into TurboTax and yet have the amount reported there split between 2 properties?" then the answer to that question is that you enter the one Form 1099-MISC as two 1099-MISCs, each with the correct rental income, making sure the sum of the two rental incomes reported adds up correctly to the amount reported on the 1099-MISC. The actual detail that you enter into TurboTax for these "two" 1099-MISCs is NOT part of the income tax return you send to the IRS. All the IRS sees are the numbers on Schedule E and the sum of those two numbers is the amount reported on the 1099-MISC.
