GMAT Sentence Correction (SC) | Re: A team of researchers reported that five endangered birds species had

We can start with parallelism. When we see "had resumed nesting OR," we have two choices for what follows:

1) We can use another past participle to continue the past perfect set up by the word "had." A and B both go this route. ("had resumed . . . or investigated" and "had resumed . . . or begun")
2) We can use another verb parallel to had. We can continue the past perfect by repeating "had" ("had resumed . . . or had investigated"),