The generally held opinion in Fandom, is that the robot Cylons turned on their masters, and exterminated them, and now want to exterminate all other life in the galaxy. One of the reasons for this is stated in "War of the Gods, part II" when Count Iblis appears within Baltars cells, and during the conversation, Baltar states that the Reptilian Cylons were "Overcome by their creations" (However, how much does Baltar actually know? Was he really given access to Cylon secrets and news?). This, and the fact that Count Iblis's voice is the same as that of the Imperious Leader make a convincing arguement, with Count Iblis certainly having something to do the whole mess.

Perhaps the Cylons encountered the Count and decided to follow him, and their immortality is the robotic Cylons. And this happened not very far away from the time of the beginning of the Thousand Yahren War. Coincidence?

Unfortunately, we will never know.

However, it is interesting to note that the books still retain the repitilians Cylons, and the robot models are not yet an integral part of the armed forces.

So what really happened?

I can not answer that, but I am actually against the Robots turning against their masters theory. A lot can be infered by Baltars statement, and it needn't mean being extermination. Perhaps, during their Cybernisation period, the Cylons decided to do without their living bodies and instead transfered themselves fully to the robotic bodies - heart and soul as it were. When the last reptile was transcribed, there would be no need for the living bodies, and they could be destroyed. Obviously, this would end up not as the great deal that it initially seemed - especially to those who would become Centurions - and thus they could have been overcome this way.

Or maybe, as a race, they did die out. Once the robots were done, they might have thought that there was no need for themselves anymore, and simply died out. Some creatures have the ability to will themselves to death, and this might have occured.

If Count Iblis was concerned, then anything might be possible. He might have persuaded them as a race to die out, or something. Maybe there are real cylons still living out in space somewhere, refugees against their own race.

I just do not belive that they were killed by their own robots. it is too simple and easy, and loses all the mystery.