I am not sure whether I should use past simple or past perfect here:
I could've met her when she was in the city, but unfortunately we didn't talk at that time and later when we resumed it turned out she had been here but I hadn't known / didn't know about that.
It's "I hadn't known", because the speaker's ignorance was contemporaneous with the fact that she had been there.
Your sentence isn't perfectly clear. We don't know if you're describing two missed opportunities, or a situational irony.
SITUATIONAL IRONY
... later, when we resumed, it turned out that she had been here all along
With a temporal phrase like all along or for quite a while, you can eliminate the ambiguity of the past perfect, which might be understood to mean "had been here again briefly for a visit and had left again":
TWO MISSED OPPORTUNITIES
... later, when we resumed, it turned out that she had been here (that is, had been here once again for a visit)
