Disclaimer: I know next to nothing about modding main, hopefully someone else will chime in later.
My guess is that just merely having your effects_models folder with the file is not enough for your mod to see it. You never added it as an asset so it's still using the one in main.
This is a tutorial for adding a custom terrain, but try following the same process for the animation/model. You create a package and then import the resources to that package.
http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=549788When you are replacing the file in Main\Assets\Effects\Effects_Models\ it works because the game already knows to look there for the model.
Also I would think the folder you should be using is the following to match MAIN.
%Game%\Data\Public\My_Mod_blah_blah\Assets\Effects\Effects_Models\
Although that might be optional so long as you import the asset.
Keep in mind your mod is stored in 3 places.
/Data/Editor/YourMod
/Data/Mods/YourMod
/Data/Public/YourMod
You could run into a *requires developer mode* type roadblock here. This is the current problem when importing audio files as well.
I'd try this for you but I don't have access to my editor at the moment.
EDIT: just to add, even if you are able to import the asset I'm not sure that's going to help by itself anyway. The game being dependent on main is still always going to look at %Game%\Data\Public\Main\Assets\Effects\Effects_Models\ without some sort of change to the code somewhere.
I assume your goal with this is to make it distributable as part of a bigger mod?