If the mortgage was secured from the equity in rental property A then yes the proper treatment would be to allocate it to property A. As you are required to list the addresses of rental properties, and as the address that secures the mortgage is most likely listed in Box 8 of your 1098, this would be the least complicated way of taking the mortgage interest deduction.
If you wish to allocate it property B, or to both of the properties, which is not unreasonable, since the mortgage proceeds were used to purchase property B, you need to do it in a rational and reasonable method.
The best methodology to determine the proper allocation would be the current market value of the properties. You would know the value of property A based on the documentation you had to submit for the mortgage. You would know the market value property B since it is a recent purchase.
Once you choose a method, you must maintain the same method. You cannot change the allocation year by year for what would yield the best tax savings.
IRS tips on rental real estate
Rental real estate and taxes per TurboTax
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