I'm not exactly sure what you mean.
If this doesn't help, please send me a link to your app or your appid.
If in your original tour you have reordered your points using the Organize dialog, the data in your layer won't in fact be reorganized. Instead the order configuration is stored at the application level. So by design if you create a new application with the same webmap, your data won't be organized the same way than in your original application, you have to redo the work a second time.
If you have dropped the layer in your webmap and added a new one, the data can become messy. In the Organize dialog, using the bottom right button "Reset order and hidden points" should do the trick.