All right, since I got no reply to my question I decided to deep dive into this myself and I finally found a solution, which is actually really simple and doesn't require any regeneration or save file reverting. So if you have similar problems, just do the following:

- stop the Factorio server if ...

Hello,

I'm running a Headless Server on Linux. After update to 2.0.9, I cannot connect to it from game without the Space Age expansion (which I don't have yet), it says that I need to activate quality, elevated-rails and space-age mods and I am unable to connect to my server. I have not re ...