It depends, if you are using both as your residence, there's a possibility you may own two apartments. But if you are planning to rent one unit out, you are not allowed to do so. Some people in HDFC buy two neighboring apartments and connect them. You have to check with the board, but I know in the building were I have sold, it's a possibility.
The main rules in an HDFC are, it has to be your primairy residence, you have to fall within the income guidelines and renting is possible 18 months out of 5 years, but you may not charge more then 10% over the maintenance. This is to make it impossible that the apartments are bought as investment property.