Your sentence isn't perfectly clear. We don't know if you're describing two missed opportunities, or a 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)