I will summarize the current state at Deutsche Bahn: Aktuelle Verkehrsmeldungen
The following long distance lines are currently closed:
Köln - Wuppertal - Hagen - Dortmund (some trains take another routing)
Köln - Bonn - Koblenz (trains are routed via the right Rhine line avoiding Bonn Hbf)
Köln - Brussels (international trains)
Dresden - Decin (international trains)
In addition a lot of local lines are damaged and cannot be operated.
In many cases a bus replacement service also cannot be operated so ... for the time being it seems like the best option is to stay home and wait until things get better.
I remember a few years ago back in Spring of 2013 there was bad flooding and I remember several replacement buses that went on for weeks as they fixed the right of ways. That time the important lines into Austria and Italy were closed in Germany near Obersee and Traunstein. I also remember some really wonky detours in the Berlin area, I couldn't tell you the exact route we took but I'm pretty confident we went via Dessau or on some other secondary line. It was a great time to collect new and different milage.