@Gothix First of all, you have to know that the conquest of a city is a complicated achievement, there will be several steps and battles before it, so, will not happen in a day but it will require a lot of time and effort. In that case, it is up to the guild that conquest the city to decide the fate of the houses and citizens. These could be some examples but remember that is a topic that we will be implemented in the future:
the guild could decide to expropriate all the enemies' houses; in this case, the citizens will have a certain period to collect a part of their stuff, and then they will be forced to find another dwelling.
it could decide to levy taxes to all the "foes" that will choose to stay in the city.
Anyway, you have to remember that the concept of possessions loss is different from the other MMO, in Fractured, with its horizontal progression system, everything will be re-obtain in a relatively fast way. The most important things that you will need for in-game progression will be the equipment crafted in the city buildings.