We finished the first scenario of the campaign, having completed the mandatory objective. Upon doing so, the app prompted us to an option to save our current board state, before moving on to the setup of the 2nd scenario.
According to the image shown in the app for the 2nd scenario setup, the ROIs are vastly different to how they were upon finishing the first one (despite saving our progress). Are we supposed to reset the map completely, or fill the ROIs based on our previous progress?
Did you load the saved state and the ROIs were different? If so, then there maybe a bug.
If not, then you already answered your question: The save specifically tells you to mark the ROI states. As such you should continue that.
The default Mission setups also show all facility tiles in the default full green state. But you simply continue with what you have. The ROI are no different.