To make a keyboard go silent, unplug the USB cable from the Raspberry Pi, allow Box Of Stops a moment to detect this (10 seconds is plenty), and plug it back it.
Whenever Box Of Stops detects a new device, the first thing it does is send a Midi Panic, or Stop All Notes, message to it. For anything to work with Midi, the controller (Box Of Stops) and the synthesizer (or keyboard) need to agree over which notes are playing. Box Of Stops is just making sure of this, by setting that requesting no notes at the start.