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[utunnels]

They grow back. Different trees indeed (there were not birches last time, but this time I saw some white trunks).
And yes, it removed the soil layer. It didn't make craters, but smashed the entire area flat (there were murky pools and channels I made before, but they were all gone, the entire area was smashed down 1 z level revealing the stone layer below).

[PatrikLundell]

Hm, so you've managed to remove the ground, but DF still think it is there, at least for tree purposes.
The only thing I can think of is painful indeed, namely to build a wall on all former top soil level tiles. That ought to get DF to realize the soil is gone, but I wouldn't be totally surprised if it actually would require channeling to get the message, which raises the thought of the dwarfy alternative: Obsidianize the whole thing and then channel it away.
I guess that means building a floor/bridge matrix over the whole thing (or possibly just a test area) with walls that are high enough to cover the altitude range, and then obsidianize all those layers before channeling them away again and removing the matrix (unless you want to keep it).
A huge undertaking, though, with pump stacks and drawbridges for both magma and water (well, magma could be let in from the side, I guess). Come to think of it, you have to do it piecemeal, because you can't pump magma fast enough to cover the whole area because of evaporation.
A positive side effect of this semi mega project is that you may create a magnificent waterfall from your water pump stack once done

[utunnels]

Hm, so you've managed to remove the ground, but DF still think it is there, at least for tree purposes.

Yeah it's strange. Because I even tried the infamous tiletypes command.
Next time I will try channeling instead of cave-in.

[Albedo]

This used to be caused by (among other things) saving the game during the fall of said items. For some reason, the game didn't save the "gravity" effect on that item, just it's position in xyz space.

Not that that solves the current situation, but if you think that might be how you got there it could avoid it in the future. <shrugs>

[NullForceOmega]

Hm, so you've managed to remove the ground, but DF still think it is there, at least for tree purposes.

Yeah it's strange. Because I even tried the infamous tiletypes command.
Next time I will try channeling instead of cave-in.

Cave-in, there's the problem right there.  Cave-ins cause a lot of weirdness, and should be avoided like the plague they are.  I've done some science on the issue and when you perform large or multi-z cave-ins a lot of tile data gets messed with.

[utunnels]

Yeah, I have already ditched that fort and started a new one.

Before that, I even tried building some floors. But trees just grew on the floors. LOL