I had changed from the "Steam Version" of Factorio to the "Normal" version because the only thing that Steams additional have is "Cloud Saving" and I don't need this feature.
The little Problem is now: every time the Game client run an update, the achievements "are gone" and I get it again, and again and again
I don't think this is a bug, simply because you may have disabled cloud sync. Cloud sync may have been responsible for carrying over achievements across versions.
"Mist"
I don't want to use Steam only because of this.
Sometimes the Steam Client went "amok" and "use virtual" all the available Disk Space on Linux so you can't save anymore. You must do then a kill -9 or 23 to stop steam. But this stops the Factorio process too...
Hello, can you post your factorio-current.log, please?
My theory is that there is an error on writing to achievement.dat file due to maybe file permissions getting corrupted, so deleting the file and letting the game create new one would fix it - but if you do that, you will lose achievements you already unlocked. In case you care about that.