The Duplicate Protection was in first place applied to the exotic engrams from Xûr, so you will get a guaranteed new one which you havn't unlocked. Also the chance getting a duplicate was reduced by the half if i remember it right.
Not true. Xûr's fated engram has always been a 100% chance to get a new exotic you don't own yet. Regardless, in the past couple weeks, I've been getting exotic drops off of enemies multiple times a day, and each time it's a bloody Y1. Something's up with that.