Our train to Germany was cancelled for today and we were told the only was out is flying. We have made train reservations for Wednesday and they may be cancelled also which will cost us over $1100 for not making it to Freiburg to use the apartment we have reserved.
The latest message from ÖBB says:
Update 10 (16.09.2024 19:31) Weather-related travel warning
Due to the current weather conditions in Austria, deviations and delays in train services are to be expected from 13.09.2024. up to and including 19.09.2024.
[...]
No train services between Vienna main station and St Valentin [i.e. between Vienna and Salzburg or Passau] until 17.09.2024, 23:59
[...]
That means they are planning to resume train traffic towards Germany from Wednesday; but of course that also depends on how much rain falls tonight and tomorrow and what effects that has.
So, personally, I actually would see if I couldn't fly to Zurich or Basel and go from there by train to Freiburg or rent a car to Salzburg and transfer to the train there (the Flixbuses from Vienna to Salzburg are unfortunately already fully booked).