I think it will come back! Missing only under load is a sure sign of fuel starvation, not water. If it were water it wouldn't matter if it were loaded or not, it would sputter constantly, especially at idle.
Since it only sputters under load it is a clear indicator the the engine's fuel demand/requirements go above what it is able to get. From there you just have to figure out why it isn't getting enough fuel, fast enough. It could be anything in the fuel system, from the tank outlet to something in the injection pump itself.
Someone dropped a piece of plastic wrap about 2" x 3" in my tractor's tank before I got it, but it worked just fine for a long time. But one day, it shifted and suddenly it wouldn't run correctly. I traced it back to the tank, and even after I took the petcock off the bottom of the tank the fuel just dribbled out. A little probing with a thin wire with a hook, and suddenly a corner came down. I pulled on it, and then the fuel shot out! Has worked fine ever since.