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I am confused regarding why some provinces become occupied after a sucessful seige, while others become conquered. Playing as Sweden in the 1792 scenerio I attacked Denmark. They appealed to Britain and Denmark became a protectorate of Britain. I was sucessful in conquering Zeeland, Jutland, Holstein and Hanover, all of which became solid colored Swedish blue. I also beseiged Trondheim, but my sucessful seige only caused it to become "occupied", with crisscrossing red (British) and blue (Swedish) stripes as well as white (neutral?) stripes. When I occupied it there was a barracks being built and no units under construction. I was able to realocate labor, but could not order units or developments to be built. I had a depot in the province, and it counted as one of my "cities". After a few turns, the province began to produce an infantry, with an artillary to follow, although I did not order any units to be produced. When the barracks was completed my depot vanished, production halted on the infantry unit (it showed zero turns to completion, or even negative numbers, but was never actually produced), my depot vanished, and I lost 4 empire points.

My questions are:

1) why do some provinces become fully conquered, while others are only "occupied"?

2) What can I do to convert an "occupied" province to a conquered one?

3) Why did things worsen when the barracks was completed, and is there anything I can do to prevent it?

Any help that anyone can give me would be greatly appreciated. Thank you.

Conquering these multi-area minors can be tricky. It looks like the capitol of Denmark migrated to Trondheim somehow, preventing a full conquest (since it was a British protectorate?).  The way you get it would be to impose peace on the British, and get them to free the protectorate. Then you could take it in another war (I think...).
 
As for the barracks situation going on, I don't know.