When running your program, consider that MPLAB X IDE operation connects to the hardware tool at runtime (Run or Debug). Consequently, settings made in MPLAB X IDE are passed to the tool only at runtime. Settings changed during a halt are updated only when runtime is initiated again.
To always be connected to the hardware tool (like MPLAB IDE v8), see Tools>Options (MPLAB X IDE>Preferences for macOS), Embedded button, Generic Settings tab, “Maintain active connection to hardware tool” checkbox.
See also Program a Device.