It does say paired, and I have been trying it with just the one joycon connected. I have 4 joycons; 2 left, and 2 right. The software works with both my left joycons, but the moment I try it with either of my right joycons, it will show the joycon on the screen when it opens up, but then insist that I've disconnected it whenever I try to chenge color, backup SPI, or anything similar. It's honestly quite bizarre.
Thing is, the joycon works in every other sense on my laptop. It shows up as connected, shows up under my connected controllers, and I've even been able to use it in games. For some reason though, the jctoolkit software will only work on my left joycons, and not my right ones... ¯\_(ツ)_/¯
Hmm that's strange then. I just tested connecting only the right one and it works (all functions).
You tried removing both right joycon from settings and then re-pair only one and try the toolkit?