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[PatrikLundell]

A good question, RocheLimit... That's one of the parameters I'd probably look at if azrael4h is desperate enough to provide a save link.

[azrael4h]

One thing that may be happening, if they're spawning in dead, is that the bodies are being deteriorated by deterioratecorpses, which I run every time I play to get rid of vultures and keas. So the bodies may be destroyed at this point, making them unavailable to retrieve. I know that dead unnamed units disappear from the units list with that active.

It's an already buggy save, with phantom trees collapsing on the surface constantly several z levels above ground. I think they're trying to spawn where there's no longer a hill. Or maybe it's because the entire map was on fire at one point. There are empty spaces scattered all over with solid soil below them, and floating corpses and logs in similar spaces that I can't reach. So I just want to retire it at this point.

[PatrikLundell]

Trees spawning and collapsing is a known issue. As you've seen it can happen under some (unknown?) circumstances that DF doesn't realize that trees and the soil beneath them is gone. Usually this involved cave-ins initially, but probably not always. I think DF believes the trees are due to grow, grows the non existent trees, and then the trees make a Coyote & Roadrunner realization that they're not standing on anything.
It ought to be possible to detect such things and "disable" the bugged trees in the list of plants on the embark, although I'm not aware of anyone having tried that.

I doubt corpse removal has anything to do with it, as corpses are not the creatures, but more the castoff body of a former creature, so the body can be raised as an undead while, at the same time the (citizens only, possibly including residents) creature (the "soul") can rise as a ghost.

Edit: I've looked into the tree cave-in issue:
I managed to create the situation by caving in a large part of the surface (about 40*40) by digging away the soil beneath, build a support, channel away the connecting surface tiles, and cutting the adjacent trees that kept supporting the whole thing with their twigs.
After the cave-in there were a fair bit of collapsing happening, and another indication of something being off was that the roots of some trees close to the edges of the cut area remained (roots magically disappear and are replaced by soil when trees are cut).

I checked the difference between a normal tree and that same tree after it has been cut down (it isn't removed from the plants.all array), and the difference was that the pointer to "tree_info" was null (it's null for saplings as well, by the way).
I saved the game at this stage.
I tried setting the tree_info pointers to null on all trees over the right half of my collapsed area, and all collapses thereafter were over the left half of the area. In addition to that, the left half sported some leaves and fruit on the ground in the same manner as when you dig out the roots under a trunk.
I then went back to the save and set the pointers to null of the left half, and collapses then happened on the right one only.
It can be noted that just setting the pointers to null did not remove the roots that shouldn't have been left in the soil.

[Melting Sky]

I think multi-tiled trees are a huge part of the puzzle with the various pathing, missing units and phantom siege bugs that currently plague the game. This is a very nice work around.

[lethosor]

I really doubt trees have anything to do with units that aren't on the map, and it should be obvious if they're blocking units that are on the map.

knedl thinks that this can be caused by saving/loading right after a caravan or siege shows up, although I don't know if that's the only cause or not.

[lethosor]

A bit late here (sorry), but I'm looking at adapting this script for DFHack 0.43.05-r2.

[RocheLimit]

A bit late here (sorry), but I'm looking at adapting this script for DFHack 0.43.05-r2.

No need to apologize, Lethosar.  If you could get this script to work for 43.05, I would be extremely grateful.  Albeit with limited testing and scripting knowledge, I have been unable to make it work in 43.05, and had begun viewing this script as only useful for older forts.

[lethosor]

It seems to do what it advertises for caravans in 0.43.05, although it doesn't seem to handle caravan items properly, and the merchants don't appear to be doing much (although that could be due to the caravan being fairly old in this fort). I haven't been able to find broken sieges/wildlife/forgotten beasts to test, but I figure a script that might work is better than no script at all (and I think it's worked for some people that I suggested it to recently).

[PatrikLundell]

I've made a single test suite of knedl's suggestion by having a save at the beginning of a season and then save immediately when a siege shows up. I tried using both regular and quicksave (which shouldn't make a difference), but neither caused any problems. Obviously, that doesn't mean saving can't cause trouble, only that it doesn't automatically result in broken sieges.