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After overriding a theme's breakpoint definitions, trying to modify the media query values appears disabled when trying to update from the group admin page:
admin/config/media/breakpoints/groups/my_theme
However, after overriding the breakpoints, it is possible to update the values through the main admin page:
admin/config/media/breakpoints
It seems like a bug that the media queries can be modified through the main UI, but not the group specific UI.