Thanks for those suggestions. Transferring militia into SHQ then scrapping them returns the manpower back to the city population. I now only have to upgrade my logistics to be able to get the militia units back to SHQ by strategic transfer - fun and games!

Enjoying the game immensely. Logistics can be hard to understand but getting there. Can militia units be disbanded? I annexed two minor countries and acquired a large number of militia units which completely disrupted my logistics. There doesn't seem to be any way to disband them.