[Edi]

Did your armies move into the province where the battle took place from somewhere else? Because if they did, that would explain it. With GoH up, or in the case of prophets and pretenders, the hit points for units are calculated based on the values that are correct for province of origin. Afterward they drop to reflect the values of the province they moved into.

What I started wondering about is if you move a pretender from high dominion to lower one, he uses hit point values according to province of origin, gets wounded in battle but survives and then the dominion penalty kicks in, could it kill him? Because for example site effects can kill units wounded in combat before the healing phase.

The dominion morale penalty is stranger, so the game files could be helpful in that regard.