After quite some time, i wanted to play Fallout 4 again. So I went ahead and made sure, everything worked as intended
I got every mod enabled, made sure the dependecies worked as they should and deployed all the mods and made sure that all the plugins were in the correct order.
Now, after making sure everything was green and looking as i remember as it should like, I started FO4 - and well, no mods were installed aparently. I got the message that there were mods installed and after i accepted that no achievments would be earned (which was still weird - after all, i got a mod installed that should enable me getting the achievments), it showed that basically every mod that the save was dependent on wasnt there. But i did not disable any mods, and it especially showed mods being not there that definitly were enabled and deployed and so on.