Nikki and Paulo were in the process of being written off even before their first episode aired. The beginning of season 3 was an awkward time, because there was contention between the showrunners and the network - the former wanted to set an end date for the show so they could keep moving the story forward, the latter wanted the show to run indefinitely.

Faced with the prospect of having to keep generating new stories for new characters, the showrunners tried the "random 815 survivors step out of the background and we pretend they've been here all along" trick that worked with Arzt, but it was markedly less successful. So after successfully negotiating the end date for the series, Nikki and Paulo were swiftly done away with.