Actually, in Spain very few churches belong to the city, region or state. Only desacralized churchs or convent turned into museums or cultural centres are not owned by catholic church. For the moment they are not relevant in the organ world.
Talking about organs the most famous example is the Bosch organ from the Royal Chapel in the Royal Palace in Madrid, which belongs to Spain's National Heritage.
Coming back to the nun's issue, the fine was finally reduced to the amount of 1,170 € (it was collected by crowdfunding in very few hours)
http://www.elmundo.es/andalucia/2017/12/19/5a38e31246163fd8418b462e.html