The nephilim are a mythical race in the Bible, not a civilization.
The Nabateans were a fairly late group. The culture seems to appear about about 400 or 500 BC.
There were some very ancient urban civilizations in Arabia, but not much is known about them. Remember that Mesopotamia, the Indus civilization, and Minoan Crete were very much lost civilizations - although there were some digs in the mid-1800s, not until the 1920s and 1930s did historians put together sufficiently coherent pictures of these ancient civilizations to establish their existance in the public mind.
Iram/Ubar probably refers to some city, but it's lost, so there isn't much factual anyone can say about it until it's found. It's difficult to discuss such things in an almost total absence of data.
One of the problems here is that when Islam arrived in Arabia, it swept aside the pagan past. In doing so, a good deal of heritage was lost - religion, myth, and historical accounts, in civilizations of antiquity, were highly intertwined (as can be seen with the Bible).