She was gone - her not being there was a past event. She might even be there now - at the side of the speaker - but sometime in the past she was not there.
I looked for her everywhere but she was gone. Then today she knocked at my door as if nothing had happened.
She is gone - that she is gone is being noted in the present moment AND she is most definitely not at the side of the speaker.
I can't find her and I have to conclude she is gone.