I remember of playing homeworld when I was younger. I read the whole history but there is a small detail that escaped me: They found the ancient ship in the desert, which was the clue to prove they weren't from that planet. But it seems that they were brought within this ship to Kharak, so how did they forget it?
I've thougut about the following hypothesis:
People brought in the ship were completely ignorant of what was hapenning. And little after being in the planet, started living a pre-historic life and after some centuries of development, they finally could find the guide stone.
Loss of memory due to some kind of effect, which doesn't seems so justifiable because the narrator of the first video says "an ancient word, older than the clans themselves: Higaara, our home". I guess that going from a pre-historic age to an age similar to ours wouldn't make possible to say the age of that word - perhaps it would be possible to deduce the age of the stone, but the age of the word seems kinda different.
They came in a different ship which didn't revealed too much of their history, but that doesn't seem to justify how they forget that they came from a different planet. In the booklet that comes with the game, it's written that they found differences between them and the planet creatures due to patterns in the DNA: Planet creatures shared some traits in their DNA's, while they had none of those. But it seemed to point that this was the only clue to their status as aliens to that planet.