With old posts, I'm not sure if the recommendation is to start a new topic or use the old since it's an exact match. I'm erring on the side of not starting a new topic, but will happily do so. This is still an issue, and I'm surprised more people haven't run into it? It happens 100% of the time for me when editing geometry. Here's a trivial example, and you can reproduce in the attached:
- edit the sketch, delete the circle, make a new circle, close the sketch
- edit the extrude, select the new circle
- go to manufacturing, edit the 2d contour
- when this dialog pops up, select "Yes" to [supposedly] remove the reference to the non-existent geometry

- but then note that the geometry is still there, but with a highlighted error

I noted people saying the behavior might be OS dependent. I'm on a Mac. Maybe part of the issue is alignment of exact terminology? Technically I guess the geometry is not there anymore, as Fusion indicates that the existing chain is missing selections (geometry is removed). That said, when I see this dialog, my intuition is "Fusion correctly realizes that former geometry no longer exists, and I would indeed love if it removed the toolpath geometry associated with it."
Essentially I'd like to "start over" with respect to everything except my selections for e.g. tool, roughing passes, linking, heights, but to provide new geometry updated with my changes to the model. I frequently am moving fast, select the new contour, and then go to save and encounter this:

Then I go back, see that I actually have 2 contours selected now and delete the one with the error. I guess technically you can click "chain" select nothing, click OK, and Fusion gives the same warning but allows it... so it is possible to manually recreate this. I think it's not clear to me what the benefit is of "removing geometry" that still leaves an error, or what the design-intent was for how this helps. I could also see this becoming more helpful with options: "Missing geometry, what would you like to do? [Remove reference only] [Remove reference and path]?"