I'll see what I can do to dig up information for you.
I am a bit far away from the Danube, but my impression is that an early September trip will still meet with chaos. Even if the water has dropped, you will likely encounter a lot of mud, if not badly damaged paths, trails, and roads. Moreover, the villages may be in no shape to accommodate you.
This does not mean that you need to cancel your trip. You just may want to take a route further away from the river.
Like I said, I'll see if I can find hard core information for you.
Cheers,
Jamie