Bit late, but small note for anyone else reading this: This is (as far as i've discovered) only an issue with the HEAVY CARGO SHUTTLE. The regular cargo shuttle seems to be fine.I've never been able to land a heavy shuttle. 10/10 failed, so thats enough for me to not bother anymore.

Another shuttle hint: sometimes the personal shuttle uninstalls itself when toggling hover mode. This might be a minified (modname) issue. Do NOT "place" the personal shuttle directly on your shuttle bay. This will for some reason delete the shuttle bay. Place it somewhere else, draft the shuttle, fly it over to the bay again.

Not a solution, I know, but it's something to avoid at least. Id suggest not using the heavy cargo shuttle for anything but caravans.

About the issue with the "install shuttle" on shuttlebay: the game conciders the shuttlebay as something that is occupying the build space at those tiles, despite letting you place a building there. So for the game, the building is in the way and gets removed before the "new" building is installed.
And yes, the way you described it is exactly how it works, no other way.

What I found out myself so far is that there are certain restrictions when using the heavy cargo shuttle:
- You must have loaded both the ground, space and world map at least once.
- Your shuttlebay must be free of movable items (stuff on the ground, installed lights etc does not count) and also completely clean, aka remove every blood stain that is below your shuttlebay!
- when landing the shuttle, do NOT! use the time compression.

My guess is that the time compression is the main problem. So far, I have send up a dozen heavy cargo shuttles that way and I lost none of them. This still can be sheer luck, but by the rate it went wrong before I doubt it to call it just luck.

I have the same problem: all the shuttles i sent on my space station disappear on landing. This include the cargo loaded except for the colonist.
Does anyone have a solution for this? Could be some other mod interference? By the way i'm still using the version 1.0

https://steamcommunity.com/workshop/filedetails/discussion/1909914131/1750149787518674676/

Posted a pinned thread for you guys to report this and a form to fill out. When you find a cause let us know there.

We need a mod list, and an error log, if one exists. We can't help when it works just fine on our end, because we need to reproduce it to fix it.

Is it Minified Things that causes this? Try turning it on and off and see.

Are you all using 1.0? (I am and it works fine.) Or 1.1?