When you replace a religion with from from a mod and copy over all the referenced files in the religionsinfo.xml you end up with a religion which uses the new icons in the world builder, on a civ screen and in the civilipedia but not on the world map, there it uses either the icon of the religion you replaced or of a corporation if its an extra religion.
I had a look at the religions tutorial and it didnt seem to address the problem, but it is obvious that the problem is workable as everyone else seems to manage it.

If I understand correctly what you want, you need to look in Assets/Art/res, locate the GamesFont and GamesFont_75 atlases and replace the the icons there.

If I understand correctly what you want, you need to look in Assets/Art/res, locate the GamesFont and GamesFont_75 atlases and replace the the icons there.

but the better question would be, HOW???:p