I have gone to 2-2 to get clearstones, but after getting all the geckos, they do not reappear. I tried moving my world tendency to black, but they still have not returned. Any suggestions?
Have you defeated all the bosses in that world? the geckos reappear when a boss is defeated.
Gecko's spawn a limited number of times, Once with no killed bosses (if I recall correctly) and one more additional time per each dead boss in that world.
I believe you're exactly right. Thanks for breaking it down more for them, I realise I was a little vague in my response.
If you haven't killed all the gecko's in world 2, and just the ones that spawn at the nest in 2-2, the one that spawns near where you get the DBS usually drops chunks of clearstone and hardstone. The one near the second ballista might too.
He mentioned above that he has beat all the boss demons and killed all the geckos, fortunately there are some other places to get this drop: http://demonssouls.wikidot.com/upgrade-quality
I suggest not bothering with raising your luck as it doesn't increase rare drops appearance, rather, it just increases drops in general's rate of appearance.
I do suggest trying to farm them in PBWT, just beware of phantoms.