Here's a solution:
Assume you have properties A, B, and C.
a) Enter the 1099-MISC just as you received it, but enter only the Property A information, and only its proportionate share of rental income.
b) Then create a "substitute 1099-MISC" with the information and proportioned rental income for Property B.
c) Then create a "substitute 1099-MISC" with the information and proportioned rental income for Property C.
The process for creating a substitute for a form you did not receive is in Djay43's answer in the following thread:
<a href="
https://ttlc.intuit.com/questions/2635641-how-do-i-file-1099-misc-without-a-1099-misc" rel="nofollow" target="_blank">
https://ttlc.intuit.com/questions/2635641-how-do-i-file-1099-misc-without-a-1099-misc</a>
(Of course in contrast to those instructions, instead of reporting the income as "miscellaneous income," you would create 1099-MISC's with the income as rental income.)
