I also tried closing the Tool, disconnecting my left joycon and leaving my right joycon connected. It pops up with a black joycon in the GUI and it still says "Joycon [L]".
So I got my Left and Right Joycon connected to the Bluetooth, they both say they are connected, but when I launch Joycon Tool it only shows that I can edit the Left Joycon. How do I edit the Right Joycon?