had did not (verb)

I sent this question in under anonymous, but I didn't want to continue to come back to this site in hopes of finding an answer, since this question is pretty urgent. I am a graduate student and am currently studying the usage of the phrase 'had did' which violates the prescriptive rule of (Had + p.p.) for the past perfect tense. During my research, I have noticed when this form is placed in a negative with a verb trailing the entire structure, it seems right. i.e. The research I had didn't help. My question is two fold. Is this correct from a prescriptive standpoint and if so, why? Thank you ahead of time.