You do not have to backshift past tense verbs, so you could say
She asked me what we were talking about.
or, to backshift,
She asked me what we had been talking about.
You would choose to backshift when you want to emphasize that the reported action was already in the past in the original utterance.
(Note that the first version is also the backshifted version of What are you two talking about? and unless you backshift for the utterance you ask about, you are not emphasizing that the original utterance was already in the past.)
When you backshift your original sentence, you cannot avoid using the past perfect progressive.
As Bill J says, the use of the contracted form we'd been talking about is
Perfectly natural and reasonable. The past perfect is used here because our talking was anterior to the time of the utterance.
This is not that difficult a concept and is routinely explained on ESL websites. See, for example, English Club.
past continuous --> past perfect continuous
Example from English Club:
Wayne said, "Were you watching TV when I called."
Wayne asked if I had been watching TV when he called.
What is not usually reported is that the backshifting of past tenses is optional. Thus, if you do not want or need to emphasize that 'watching TV' was already in the past, you do not have to backshift.