Well, one of the shittiest and most destructive things that could happen to a UAV happened to me today. Accidental low-battery LAND failsafe set my 3DR Y6 down... into a pool. I retrieved it immediately and disconnected the battery. Now I'll wait for a few days for it to dry out before doing some system tests, but I'm curious what your expectations for system function will be at this point. Crappy? I think so. It was smoking when i pulled it from the water. Oy.
Similar thing happened to me yesterday, 3DR IRIS+ practicing hovering and takeoffs/landing in my back yard, staying under 30' and using loiter mode and the wind kicked up 15+ knots and I decided to land and (foolishly) switched to RTL and the wind overpowered and blew it right over my pool. I switched to std and full throttle but response came too late and it just barely touched the pool with two feet and flipped then sank. The good news is the Ricoh WG-20 waterproof camera got a good show of the smoke bubbles for about a minute before I fished it from 7' down and pulled the battery. It's now disassembled and sitting in the sun during the day and under a fan at night. The only obvious damage is two rows of the 4-in-1 ESC shorted/fused and burned, but surely the Pixihawk isn't waterproof so its days are numbered.
I'm curious if any of your Y6 components were salvaged or did you have to scrap it?