Well, I see that population management was totally overlooked by RTW developers. If that's the case then the only solution is really to give back to the AI the citizens it enlisted into the army.
It's the lesser of 2 evils, although personally I'd prefer the situation where the enemy can lose the war when he's putting too much pressure on his population and simply can't recruit more troops either because of the depopulation or because of tremendously increasing unrest when recruitment is excessive (especially in type II-IV) provinces. But I'm nearly sure it can't be implemented in a mod.
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