When I'm using "WorldGen Update", I get a lot of tracks and some buildings destroyed. Some of my "roads" will also get destroyed by terrain or a cliff is suddenly crossing them. Is there an incompatibility with some mods? I was using "Regenerate Terrain", which will not destroy my stuff, but the world would be lot different and I have to deal with enemies in my base. I tried to tweak some settings with "Change Map Settings", is there now something I changed, what will cause the destruction. The generated world itself looks fine with "WorldGen Update".

Sounds like some mod incompatibility.
Which entities and tiles from which mod are missing?

The only known issue is with Creative Mod.
CM can spawn concrete without landfilling first. My script tries to properly landfill under concrete, but to do so it has to remove the concrete first resulting in entities on top colliding with water, being invalidated and removed.

I think most items which are missing are vanilla train tracks and not becaus of water, there are a lot missing on land. I have some mods running but the base is mostly still vanilla except some turrets and walls from rampage on the outskirts, but they are still there. I have a big train network with LTN and it is telling, that it can't find routes and a lot is out of reach and I saw that a lot of tracks are missing inclusiv parts of trains which where on the tracks. Some Cliffs are crossing on build land (concrete floor), too. Maybe it's alien biomes or the river option. I'll test it without river and later without alien biomes.

Edit: Example without "rivers" (same): https://steamuserimages-a.akamaihd.net/ugc/1486705342482389099/F80D9289B087B7244DDBDCE2B58F702044DECCFC/

Its "Alien Biomes", now the tracks and buildings are still there.
The issue with cliffs and pavement still exists: https://steamuserimages-a.akamaihd.net/ugc/1486705342482454027/2D6B2AFC9942F20CB44195FC2DB5DF3ECD1261CF/
Do you think it's possible to make your mod compatible with "Alien Biomes"?

Alien Biomes seems to still be working for me, both in converting existing AB maps and for adding AB to vanilla maps.
I couldn't test all the biomes that massive mod adds though.

I checked an earlier save, where I didn't changed the map settings and it's the same with the tracks. I also tried to delete all chunks around my entities, which lowered the missing parts, but it still happened. Without Alien Biomes it seems fine apart from some cliffs.

I've added a new setting "floor starting layer".
Set it to the lowest layer of placable tiles listed in the logfile by Alien Biomes. In my test setup it's 184 for "stone-path", will probably be different for you.

Yes, I already saw the update and started the test (generation takes a long time). For me it was 185 (default was 60). Still broken train-tracks/missing structures, but this time there where rivers there. I'll test without them. Cliffs on concrete is still a thing, too.
But thanks a lot for your effort so far.

[delete]

Cliffs only check for collision.
I never got to add them into the logic that keeps trees and rocks from respawning on floor tiles.

Without rivers it's still broken, but there are water bodies now: https://steamuserimages-a.akamaihd.net/ugc/1486705493715401071/F419B798A637BE4B12D9400C72B6ADCD4077B5FD/
Map settings has its default to "swamps" - I'll change it to "normal" and try again.

Looks like some of alien biome water tiles collide with "ground-tile".
Only fix at this point would be to manually write a blacklist of alien biome water tiles....

It's the same on setting "normal". The water tiles are still there. I think these are the shallow and walkable water from AB.

I did some tests and when I disabled "Inland Shallows" and "Rivers" it looks fine (both are destroying stuff). "Coastal Shallows" seems to have no impact, they are probably take from the water, not from the land.

Let me know if 0.2.2 works for you.
It should not write any tile colliding with water layer. Also contains more debug information, please link factorio-current.log

It's the same when I reactivate "Inland Shallows" and "Rivers". When activated, it destroyes structures and even stuff which should be fine:
https://steamuserimages-a.akamaihd.net/ugc/1486705560676580031/6B8353DD43A357995BC7088F75E434419312D4AC/
https://steamuserimages-a.akamaihd.net/ugc/1486705560676566436/C723F9CE33683BA385D27B6B1DAD96275A31C944/

factorio-current.log: https://pastebin.com/tDE65QG3

I regenerate now again without shallows and river to verify, that there is not a new issue with that version.

I can say for certain none of those shallows or rivers where placed by my script.
Debug: tile layers: lists all tiles it placed
Debug: floor tile layers: all tiles it tried placing on top of that
Neither of which contains water tiles.

Maybe because they are passable, they are not defined as water, but as normal terrain which collides with structures - or as special path? For me it's ok to use the workaround and disable the two features in AB.