Unit-stat modifications to the EDU are fully savegame compatible and take effect instantly, more or less. AFAIK around the only stuff that isn't savegame compatible is anything that alters the actual content of the strategy map (although the incompatibility only means the modifications will have no effect on an ongoing campaign AFAIK), character trait files (which tend to go very spectacularly screwy) and some other such peripheral stuff.

As for the chariots, back in previous edition weren't they given two HP to represent the horse team ? Mind, I guess there's a reason that got ditched. Would still like to know it though, if only because I'm a curious person.