As title suggests, for some reason I'll randomly have the shaft to go up from a surface be deleted. It's not biters up above attacking anything, and I've yet to catch exactly when it'll happen. I just know that sometimes when the shaft entrance is off screen it'll be deleted with no signs of what causes it. I've noticed it from above and below ground, even getting trapped down there and requiring a reload once.

Ores still don't seem to be generating below level 1. This bug is current as of today when I was testing it. Speaking of ores, it seems that depleting a certain spot on a patch (Like around the edges when you are only using burner drills) causes that same spot to generate empty on the subsurface below if you mine everything out before revealing the sub surface. Also not sure if intended or not but I did not seem to find a stone patch underground either .Granted with how much stone you get from the digging it's not a huge issue, but also seems kind of weird. The surface stone patch generated pretty light, which I assume was due to the same thing that causes the other resources to be generated light, but without the benefit of subsurface patches to exploit.

Do you use other mods?

Stone is indeed not generated in subsurfaces, you found the reason why.
Ores on the planet's surface have only 10% richness compared to vanilla, but the patches below have like 100% with a decreasing patch size.

well i tried to put one on vulcanus and the game crash's every time

error while runnign event subsurface::on_resource_depleted(ID 29)
unknown variable entity:scrap:richness
stack traceback:
[C]: in function'calculate_tile_properties'
S.S /scripts/resources.lua:19 in function 'place_resources'
s.s/control.lua:239 in function 'clear_subsurface'
s.s/control.lua 528 in function <Subsurface//control.lua:516>