Sessions, FX Chains, and Presets must be resaved manually after editing and reuploading an algorithm.
My method when replacing an algorithm I've created is:
1. remove the algorithm from the session
2. delete the algorithm from the H9000
3. upload the updated algorithm to the H9000
4. add the updated algorithm to the session
5. recreate the preset I was using in the session
6. save the session