I created a bug report for the issue described above; being very rare and not reproducible doesn't help in tracking down the problem, though.
However, it sounds like you have a different problem, if the disconnections are not happening due to timeouts or dead batteries, etc.
Do you have the same problem playing in single player (or online multiplayer, if applicable)?
Try doing a clean boot and then test the controllers (starting the game directly from the '..\SteamApps\common\Divinity Original Sin 2\bin\EoCApp.exe' program file, by right clicking and running as administrator).
Click Start, or hit WinKey-R, type in msconfig and hit enter; in the General tab, click Selective Startup, uncheck Load startup items (if required) and leave Load system services and Use original boot configuration options checked. Next, click on the Services tab, check the box to Hide all Microsoft services, then click the Disable All button (maybe make a note of which are currently enabled/disabled), then click OK and reboot the computer.
Run msconfig again to switch back to the normal boot configuration.
