Time, there was a huge amount of time between the Cetra first appearing, some Cetra stopping following their ways, and Jenova's arrival.
Now, if all happens in one planet, it makes sence the Cetra were killed. Had the Cetra moved from planet to planet, they would have been away from Jenova, and would have lived. Yet, without the Cetra, how does the planet would have lived?
The Planet was saved by sacrificing the Cetra. After
that, your ancestors continued to increase. Now all that's left of the Cetra is
in these reports.
The Cetra, then, must have only migrated within the planet, for them to be there when Jenova appeared.
Confirmed, the Cetra are originaly from the planet, and not from somewhere else.