Forget your map for a moment...
You need to isolate the variables.

Do you see the engrams from SS?
If not, then the mod isn't even loading correctly.

If you can see the engrams, can learn, build, and place them... Then the mod loaded correctly and your save file is at fault. Revert to an earlier backup.

This is less of an SS specific issue than it is a general mod loading issue.

Chances are on first start the mod didn't load correctly and thus ♥♥♥♥♥♥ up your world save.

So reload it and try again

Mod is there, I can see the SS Engrams.
So I'll try with an earlier backup, thank you!

I have now got it working. The problem was that first I didn't load the mods correctly, then I loaded the map and saved it. When the mods were imported correctly afterwards, I had loaded the map that was corrupt earlier.

If you have the same problem: First load the mods (.mod files and folders) correctly in and set the settings in GameUserSettings.ini (optionally also via the start command '?GameModIds=xxx,xxx,xx). Only then import the map and start the server.

Stupid mistake, took a while to figure that out.