Can pernicious anemia or severe vitamin b12 deficiency cause chronic non-specific duodenitis??

No: If pernicious anemia is treated with Vit B-12 injections the patient will be otherwise normal. If not he will have atrophic gastritis, hematological problems as well as neurological ones

Which came first?: Pernicious anemia results from the reduced gastric production of intrinsic factor. It is often associated with other autoimmune diagnoses. More commonly duodenitis/gastritis from NSAID overuse of meds like apirin and ibuprofen/Advil and infection with H.pylori causes B12 deficiency. http://emedicine.medscape.com/article/204930-overview#aw2aab6b2b3aa

Not clear: No clear evidence for the causal-effect relationship between the two. PA is an autoimmue-mediated destruction of parietal cells in stomach, resuling in impairmnent of B12 absorption. Certainly it is possible that pernicious anemia may co-exist or exacerbate duodenitis via immune process or loss of balance in duodenal fluid, or anemia. But the causal-effect relationship is not well established.