The homeland, expansion and outlying region markers that determine what levels of government you can build will be set up for your previous faction, this is because these are set at the start of a new campaign by the campaign script (not the same as the main script), you can't change this halfway through without using more scripting.
This happens when ever the AI takes a settlement, the existing goc building is damages and a new one for the invading faction is created, the script will see it like the AI has conquered control of your cities and will act accordingly.
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