Hi. I don't use smart albums but this seemed to work with regular, not-smart ones:
- I reordered some photos in a collection then selected them in the filmstrip (in your case, your smart album)
- From the filmstrip or grid, I right-clicked and chose "Mark to republish"
The photos then showed in the grid as "Modified Photos to Re-Publish." After I chose "Publish" they were reposted to my Flickr album in the new order.
Maybe that helps!