As pointed out by The Undying Nephalim on the forum, when units are promoted they lose their position in their formation. They also lose any aura bonuses. This patch fixes that.
Ideally we should check if the new and old units have formation auras, and apply or remove them. But currently only Athens' Iphicrates has a formation aura (+3 armor), and he can't be promoted, so it's not an issue.