All good RSS feed provide an unique identifier for each of their post, usually either called GUID or id. This sub-item is composed of a permalink attribute and a value. The permalink attribute receive a boolean, telling the reader if the value is, and always will be, a link to the article, or not. In the negative, the value can be whatever string.
In your case, check out the item.y:id sub-item (the y denotes the Y! pipes name of the atom - I think - namespace, no need to attach much importance to it right now): it has both permalink and value. Hence, if you use the Unique module filtering on item.y:id.value, you won't have any duplicates.