Try docking the Switch, connecting the Joy Cons to the docked Switch, and then doing a hard system reboot. And make sure to do this after you've done the latest system update. This is supposed to update the firmware in the Joy Cons to the latest version, which has been said to help with some of the desyncing issues. It's also good to have a clear line of site to the system, and stay within 10 feet if the issue keeps happening.
To do a hard reboot, you need to hold down the power button on the actual Switch for at least 12 seconds while the Switch is on. After a few seconds this will turn off the Switch. Keep holding the power button down and after more than 12 seconds pass, release the power button, then press it again once for about a second like you normally would to turn it on. This reboots the system.
The one that came with the ME/SE BOTW sets looks AMAZING in person. It looks just like the in-game Sheikah Slate. It's not a hard case per se but it fits the Switch well and protection seems pretty good despite it not being a hard case.