[KaleunMarco]

Originally Posted by Kapitän

Okay. So, does this apply to the mods that come with, for example with KSDII, i.e., I installed certain mods from the mod set that come with the game when downloading and installing it right at the beginning and haven't changed those since then ...

well, there is no set of saved config files at the "beginning" of an installation.
SH4 stores/caches certain config files when the player starts his first career mission.

after this point, deleting config files after a mod change is a universal constant.
when a player changes mods or adds new mods or even a new mod set, it is highly recommended (polite words for mandatory) that you delete the saved config files before launching a new career.
if the player does not do this, then invariably they travel to Area CTD where there is no hope, no light, only darkness and despair.