Update: Warning!
Currently doing some testing in creative mode, where I built a room underground to the limit, with some cuboid rooms removed to leave a hole. Flew away from the base till about a 1 minute distance at high speed. Upon return to the base, lo and behold … the cuboid rooms all had the terrain reset, while the hole where I removed the cuboids after placing did not reset.
Hole created by placing, then removing cuboid room - No Reset
Cuboid Rooms placed underground - Reset
Same Cuboid Rooms (some terrain removed with Terrain Manipulator from outside)
Will do some further testing with a variety of different structure parts/rooms as well as limit or no limit reached and update my findings. For now be aware that this may happen, it does for me at least on PC.
Edit #1:
Additional Info:
Initially I tested with only a few blocks underground, to then fly away and wait for 10 mins, 30 mins, 1hr, 1.5hrs to no avail. Reloading a save or restarting the game had no results either, the terrain just never reset with only a few Cuboid Rooms underground.
I decided to stay at the base with only reloads, while staying at the build limit with a huge amount of Cuboid Rooms above ground, I started to slowly increase the amount of Cuboid Rooms underground, taking them away from above ground, until a reset happened. Apparently the amount of blocks used underground causes the terrain to partially reset. I had always thought the terrain would fully reset, but this is actually not the case. At some point I ended up having 69 Cuboid Rooms underground, when I noticed a reset to have happened. Using my Terrain Manipulator, I did some investigating and found a big part of the underground room, not having terrain inside.
I then decided to not stay at the build limit, no longer using Cuboid Rooms above ground, apart from the entrance. I then started increasing the amount of underground Cuboid Rooms, until I once again noticed the terrain to only partially reset. This happens at over 60 Cuboid Rooms used underground. This also means that being at the build limit is no requirement. A reload/restart or moving far enough away from the area to unload the region is however required for this to be triggered. The result of this last test can be seen in the video below:
I still plan on some further testing with other building parts and will keep you informed on those results.
Edit #2:
Additional info:
The same appears to happen when using other building parts. Only the Bio Dome seems to remain unaffected. As soon as you reach a high amount of building parts used underground, the partial terrain reset will happen after a reload/restart or unloading/reloading the area.
Terrain which is then removed using the Terrain Manipulator will remain removed it seems. It can just be very hard to do so especially if this is required to be done from the inside where the tool does not work. Sometimes however, you can find a sweet spot inside where the tool does work (atmosphere affects player). Terrain likely starts to partially reset at the location where you started building underground.
This concludes my testing for now. All should be fine up to 60 building parts used underground. More may be possible, but becomes risky and may require the Terrain Manipulator to fix up unwanted terrain inside your underground base. So once at the tricky stage, reload often, to check. Happy building