The answer, as is frequently the case, depends on what you intend to say.
The first formulation is certainly awkward and ambiguous, but I do not go so far as to say that it is grammatically impossible. I probably would not writie it unless no other formulation expressed my meaning.
"I haven't read the flashcards that I made a few days ago" makes clear the present state (not read as of now) and the sequence of events (the making was in the past).
"I haven't read the flashcards that I have been making these past few days" makes clear the present state (not read) and the sequence (the making started in the past and is not necessarily terminated).
"I haven't read the flashcards that I had been making these past few days" is in my opinion just wrong. The "haven't read" indicates a present state. The past perfect implies a completed action or state that preceded a past action or state.