Sorry to necropost, but I'm having the exact problem, using Real Waters 2 on Skyrim SE & half of my river is missing, (not down the middle, but between a bridge and a bit further down the river where the water decides to appear again). When I get into the 'dry' spot I am under water, but standing next to it or a bit away from it, there's no water visible. I've tried reinstalling RWT2, but no luck. I'm not using any other water mod, so I don't know what's going on. If I ever figure this out, I'll post whatever I find. The reason for my addition to an older post is that there are people who periodically have this problem, which is making the game weird & maybe I can help someone if I figure things out.