I do ford a creek regularly, there’s one at the gate of my hunting lease. But it’s nothing crazy, and it’s too dangerous to cross if it’s higher than axle level.Yes, most likely the breather hose. Did you go through deep water? Did you check that they aren't cracked? You may need to raise them higher. I (lightly) milkshaked a rear diff last week due to water up to the hood, thought I was being careful, but it happens. Changed the fluid after the trail and its fine.
But I think I found the issue. I looked up where the breather hose vent is attached, checked the Jeep and it wasn’t there. Chased the hose from the diff and somebody had laid the hose horizontally up on top of the frame sort of between the bumper and grill where the plastic “Jeep” frame cover is. So every time it rained, every deep puddle, every time I washed her that hose probably took on water. I’m just glad I went ahead and did this before my diff exploded.
Besides the god awful milkshake the gears look ok. Ring and pinion look perfect. A couple burs on the spider gears. There were fine metal shavings in the fluid, but as I understand that’s to be expected and why the fill plug is magnetic.
Thanks again for all the help, I’ll update as soon as it’s back together and see if the noise has changed at all.