it doesn't matter if you occupy more than one property, as the provision of section 10(13A) states that the allowance granted to the employee to meet the expenditure actually spent on rent for occupying the residential accomodation.
In the section the word 'Occupied' is used, so if teh assesse does not occupy the accomodation & still he is paying rent he cannot claim HRA exemption. the section does not specify the quantum of occupation of the residential house by the assessee, unlike in case of a resident & not ordinarily resident. where the quantum of the stay of days is being mentioned to be called as a resident or not ordinarily resident.
So as you periodically occupying the other house, you can claim the HRA exemption u/s 10(13A).