A theory:
Humans, while on Kobol, invented a technology that allowed them to resurrect into a cybernetic host or cloned copy of themselves in the event that their “natural” existence terminated. This is what brought the wrath of the “Lords of Kobol” - humans found a way to become effectively immortal, and therefore challenge them. This development resulted in whatever destruction happened on Kobol - perhaps it was the “lords” (who were likely humans who previously had exclusive access to such technology) trying to crush the populace, or even better, a war between those humans favoring the technology vs. those that didn’t (for moral/ethical/religious reasons.)
This war resulted in the scattering to the colonies - the 13th “cylon” tribe that reached Earth maintained this technology (and were “outcasts” from the rest of the human race because of it). Either way, Kobol was rendered inhabitable, but some mechanism remained in place to prevent any kind of resurrection from happening there again. Possibly, this mechanism is what started the war: either the non-resurrecting humans or Lords of Kobol created some barrier to resurrection which caused the resurrecting humans/cylons to revolt. (The resurrection limitation was suggestion in an earlier show when they re-found Kobol.)
The members of the 12 colonies, after settling in, later found the Cylon-inhabited Earth and in an act of “ethnic” cleansing or as a follow-up to the original conflict, nuked them from orbit (presumably also destroying any resurrection technology present at the time.) This may have been a covert military operation that many of the populace was not aware of - hence the memory of the 13th tribe eventually became a legend, perhaps known as Earth as some information about its existence eventually leaked out.
Regardless, the Cylons, realizing the inevitability of future conflict with non-resurrecting humans, had developed a fail-safe in case of such an catastrophic event. This fail-safe allowed a limited few to effectively re-incarnate in a human host (sort of an inverse of their current resurrection technology). As others suggested, it just took some time for their downloads to find suitable hosts, at which point the Final 5 were born within the colonies. Humans may have sealed their own fates by nuking Earth as it ensured that the Cylons would return to the rest of humanity.
Concurrently with the events of the past 3400 years, there was a Cylon diaspora that never made it to Earth from Kobol, or perhaps made it to Earth but began space exploration. These individuals eventually found the mechanical Centurions who were at war with the 12 Colonies, possibly after the first human-cylon war. (Alternatively, perhaps the downloading Final 5 could also re-establish themselves within the Centurion mechanical sentience - based on the helmet that was found on Earth, Centurion technology was known to them.) In either scenario, the Final 5 and new-found Centurions realized that they could mutually benefit each other - the Centurions provided the diaspora/explorers/Five with access to whatever mechanical and technical resources they had while the Final 5, possibly knowing that Earth had been destroyed, shared their cybernetic and resurrection technologies and allowed the Centurions to evolve into biological beings (remember, the resurrection technology was not known to the 12 colonies until after they were destroyed - it had to have been established between the 2 Cylon wars.)
Another theory would be that the cylon diaspora/downloaded Final 5 enslaved the Centurions by placing the “free-will governors” in them, and re-established and grew their species using whatever technology or resources the Centurions had (which were perhaps limited resources, hence model lines had to be established, rather than a society comprised of distinct individuals).
Its all happened before and will happen again as long as mortal and immortal humans remain. That’s how I would write it, anyway. 