He tried to distance himself from her in the first timeline so the real veronica would not be powerful when she returned, and tried to protect her when she was pregnant, but her fake dad had already gotten ahold of her. He knew and was trying to protect her the entire time- at the end of the first timeline when he is holding her baby, after she dies, he says he never knew her real name and will refer to her as the "shadow queen". He also kills the real veronica to avenge elena