As long as your records determine how much was for which income property, then you will need to add the full amount in on one property and then take a deduction for the amount to go to another property. As long as the totals of income are reported on the return and allocated so IRS can trace them, then you should be okay. They may send you a letter of inquiry, as a worse case scenario and you can explain to them.
I would ask the payor of the 1099s to separate them for future years, even if you have to get some EINs for the businesses.
