So I have a problem: I put Germany in neutrality but when I open my game with my mod, Germany is fascist and the faction I created does not exist.

I've swapped the country's name to "Germany", from German Empire, as the game prioritises Germany's base-game history file for the tag "GER", changing the name to "Germany" causes the game to read your mod's file in place of the base-game's. 

This change only affects the site, all of the custom names you have set should still appear in game as you expect.