I am not a grammarian, however, looking online I see that the past perfect tense indicates that an action was completed (or not completed) at some point in the past before something else happened. I would say that a mere state of existence is not the same as an action which has or has not ended. If your city didn't exist, well, it simply didn't exist and you can say so.
With regard to using the past perfect, I believe this would be appropriate if one were to write, for example, "When the Normans started to rule England, the construction of our cathedral had already been completed (or hadn't been completed)." Or, to use the verb "exist" specifically, one might say, "When the Normans started to rule England, my city had existed for less than 10 years", again, showing the completion of, in this case, a period of existence with reference to another event (Normans starting to rule England).
Perhaps others can correct or clarify my comments, as needed.
