I didn't say they got destroyed, but we have a nice city in one spot and huge detailed aztec temple in other place. Now what's the point in having great architecture when there are lot of gaps (even between the two) that get filled with completely wrong terrain. Our point was having great piece of land (that's why we don't use vanilla generator).
We could and we will probably try to move what we have to another world, but main city is strongly affected by terrain form, so moving away from this world is really demotivating. The cahnce that we will find as good and fitting spot in other world is really low.
Now I don't think this happens every server restart. I tried creating world and generating it with World Border. I restarted server several times before finishing generation and it generated without any issues so this might be caused by something else than restarting a server itself.