You'd need to edit the DOM_Britain_Missions file, in the missions folder in your mod, that's where both the British and Angevin mission trees from Domination are as far as I can tell

In these files, missions are grouped into series(branches), and in the script each series has a "potential" section, where you define conditions (aka triggers) for whether a country has access to that series or not. You'd have to change those triggers, and change each mission's position, so that the game doesn't try to place two missions on the same place in the tree.

I recommend you check the EU4 Wiki's modding articles for a better explanation (especially the Mission modding page), that's where I learned everything I know about making mods for this game