Are sure you saved your game after killing PX? I mean, if you watch this clip
on youtube you will se that right after execution of PX, Niko calls Dwayne and learns from him that:
1. Niko can keep PX's mansion.
2. Niko is encouraged to hang out with Dwayne, to which Niko replies that he'll call him soon.
Which means that after completing this phone call, parking space should appear in front of PX's house, which should become accessible for you as a safehouse. Plus, you oughtta have Dwayne in your phonebook.
I'd go back to a file before that mission, but you probably don't have any saved games that old. So either restart game or forget about Dwayne. I suggest the latter. He sucks as a friend.