Say right now, your friend is asking if you know Mary. "Oh yes," you say. "I have known her for some time." You are talking about something that started in the past and continues now.

Now, let's say your friend asking about the fact that you are just back from a visit to someone that you met online. "We had talked every night for a month before I went there. By then, I felt like I had known her for a long time." You are talking about the situation that existed at that past point in time when you went to visit her. You may know her still (the visit was a good one!) but you are referring to something from the point of view of the past about something even further in the past.

If the person uses present perfect (has she done it?), then you answer the same way if your time of referene doesn't change - she hasn't done it.

If you want to refer to a past event - you asked if it was done yesterday and the answer was no - the "When I asked her yesterday [in the past], she still had not done it."

I hope these examples help.