Shaeonanra explicitly makes it sound like all they found were the twins. Aurang and Aurax are the last of their species. Unless they've managed to clone more after re-mastering the Tekne.
And the Ark did die, if the Inchoroi themselves are to be believed. The Ark was a biotechnological construct. The walls inside used to be coated with flesh. Given that the Inchoroi used to call themselves "Children of the Ark", and Seswatha referred to the Ark as their Father, I believe that by the time they arrived in Earwa, the Ark was where new Inchoroi came from. Some sort of synthetic biology engineered mass cloning or artificial insemination factory.
However during the impact, the organic parts of the Ark seem to have died, and the surviving Inchoroi lacked either the knowledge or tools to regrow them. Thus they were unable to replace any of their number, and the Nonmen slowly ground them down until only Aurang and Aurax were left.
I do believe they were basically hibernating, somewhere deep beneath the Ark, like you say.