You should not have a problem. Enjoy your train ride.
Refugees flood into Germany
Even with the bottleneck in Hungary, migrants were still making their way to Germany, just not many by train. Germany's government said last month it expected up to 800,000 asylum seekers to come this year -- four times more than in 2014. At Munich's main station, though, the arrival of refugees slowed to a trickle because of the restrictions in Budapest.
Trains between Munich and Salzburg depart from the very early mornings until late evenings essentially on an hourly basis (or even more regularly than that during rush hours). Since both Munich and Salzburg are important transportation hubs, trains pass through the two cities essentially around the clock; however, night-trains might offer inconvenient connections in terms of necessary changes or long driving time.
If you take a train from Salzburg to Munich (or the other way round) at some time between approximately 7 am and 9 pm, you will get there in less than two hours. Trains between Munich and Salzburg