The problem is the water permeated the shoe. But your application of Clorox wipes (or whatever you use on the surfaces) is only hitting the surface. I agree the solution is to submerge them again.
You might start with a pretty strong vinegar solution, follow that up with a good soaking in a mild Clorox solution at 1/4th the concentration you would use on white shirts. After they've soaked awhile, soak them again in pure water. The residual clorox in the shoes will purify the water, but the water will also dilute the residual Clorox to the point that it won't keep eating away at the shoes.
After the soaking and rinsing is done they need to dry thoroughly. You can drip-dry them in a warm/dry climate. If you're in a more humid climate, go buy a 10 pound sack of rice and pour it into the shoes.
All this might be too much for the glues in the shoes. Hopefully it doesn't ruin them. But the stink is already ruining them, right?