I don't think it's just the Joycons unfortunately, I've also had the Pro Controller lose connection completely and not work again until I put the console in and out of sleep mode. This was after it had worked perfectly for over 20 hours of Zelda, with everything set up the same way.
Uh-Oh... This really makes me nervous since it's the first time I hear people having problems with pro controller signal as well. D: I really really want Nintendo and Switch to succeed (that's why I bought it on launch day) but with quality control like this they need to step up or they will soon have lots of angry customers...