Originaly, I did have mods. I then disabled all mods, except for Space Age, and tried to reproduce the bug again, to ensure it was not abnormal behavior from the mods.
As for the steps, those I already included, as well as a video. But if you must insist:

Build two transport belts facing the same ...

I listed Space Age at the top, so yes, there is mods.
Note: It is currently late for me, so I'll test tomorrow, and edit the reply

Mods: Space Age
Viewing Nauvis from Gleba, I discovered that dragging a belt and upgrading the underground, in this specific order for some reason, made the underground disappear. Undoing it just said, it was deconstructed. The underground is also destroyed.

To reconstruct:
It works on all planets ...

There's is what seems to be a small gap inbetween the arms of the rocket silo, and the rocket itself. It seems, as if they're still holding the same place they did, before the rocket reskin from 2.0

As stated, mods. You most likely didn't have Space Age active. And as for the log? IT's too long ago for it to be present anymore, same goes for game version. Sorry.

How to replicate: I don't know. What I do know, is that it is unavoidable. You can not avoid the crash.
The mod list is the one attached, you know it's active or not if it's stated. (I'm lazy)
It's one of the three autosaves that's the newest.