5.13.3 Run Considerations
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 (MPLAB X IDE > Preferences for macOS), , Maintain active connection to hardware tool checkbox.
See also 5.23 Program a Device.