In a heave saucepan, prepare the filling. Whisk together the rice syrup, water, agar flakes, cinnamon, and salt, and bring to a boil. Reduce the heat and simmer over low heat until the agar dissolves completely, stirring occasionally, about 5 min.
In a small bowl (or coffee cup ), dissolve the arrowroot in water to barely cover and add to the agar-rice syrup mixture. While cooking the mixture at a low simmer, whisk it until the chalky color becomes clear.
Let the mixture cool for 15 min. Stir in the pecans and vanilla and pour into the prepared pie crust, distributing the pecans evenly.
Let the pie cool to room temperature and set, about 2 hours (or refrigerate for 1 hour).