1.Twelve birds had originally arrived; only six remain. .. is this correct?
2. Twelve birds have originally arrived; only six remain........? whats wrong with this?
3, Twelve birds originally arrived; only six remain.............. ? whats wrong with this
3 IMO, is the best. It'd be better if we get the entire sentence."Arriving" is a discrete event and should be in past tense.
In 1, "had arrived" demands another past event, which is absent.
2, present perfect for a discrete event is not preferred in GMAT. Also, the birds are not arriving now.
have arrived is perfect tense. Its not necessary since the next action is in present.