Are you changing the normal font or a different font? The normal font in a RichTextLabel is the font used when the text doesn't have special markup (bold, italic, etc). Its the one that is most commonly used so changing it should change the majority of the text.
If the font is changed though, I'm not sure right off. Are you saving the font as well into the .tres or is the font its own .tres file? Also, what version of Godot are you using?