I’m not sure I fully understand your scenario… How many waypoints do you have that need to be modified? Are they defined in Script or Polyscope Waypoints?
If they are Polyscope Waypoints could you put copies of the key waypoints (linked to the waypoints down further in the program) in a folder at the start of the program that is not executed? If they have clear well defined names, these could be adjusted, and then the linked waypoint further down the program would also change.
Example below. Move command inside If False node would not execute.
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