The Thirteenth's time line flow (POSSIBLE SPOILERS)

[Cilia]

It's variable as the writers see fit.

The Flood occurred 100 years ago First time, but it can't have been more than a couple years Source time. Conversely, the other Scions were called to the First a few weeks / couple months before the PC Source time, but it's been years for them when we get to there.

As for the Thirteenth, it's... unclear. Remember that by most measures time no longer has meaning there.

EDIT
Unukalhai (and I'd wager Cylva as well) were held in stasis by Elidibus until he had use of them. As I recall the Sundering was ~12,500 years ago, and the Allagans were messing with artificial voidsent before the fall of their empire ~5,000 years ago. Relative to Source time the Flood of Darkness on the Thirteenth would take place somewhere between the two.