As per the design, it should be possible to hide regions selectively by step (breakpoint). Currently if you remove a region, it is permanently removed from all steps in the layout. You don't have the region in any of the steps. As per the design it should be possible to hide regions as well, so when you initiate to remove a region, you'd be asked if you wanted to hide it (just from this step) or remove it from all steps (the whole layout).
Removing from all steps should have the result of the region being removed from the list of regions used in this layout. This is the current behavior.
Hiding a region from one step should add information to the step based overrides indicating the region is removed. The format for this should be defined (currently column width overrides are the only thing supported in the overrides data structure at least on the backend side). So the feature should be implemented according to this on both the frontend and backend.