Now that makes sense. One could make a case for Berlin's location being moved but I will defend Cologne's. I know it'd be more accurate for it to be on the western side of the Rhine but "Marburg" (where it is right now) is better regarding gameplay as you're better protected from French attacks.
Also, for some reason whenever I manually rename the cities they eventually switch back to their old names.
In Germany and Italy the only cities having the name they meant to are Hamburg, Konigsberg, Naples, Rome, and Milan, while any city named "?" keeps that name. I noticed in the rest of Europe every canonical city has its intended name except for Paris (Sens), while Mecca has "Al-Qunfundah" or something like that.