@ john_martelly....I'm planning my trip for early summer of next year, ie end of May/June, can't really do it in July. The refugee situation is a factor to contend with in my planning for Austria and Germany. To contend with, yes, still I'm going, including a week in Vienna. The situation with the border crossings has been/is whimsical, as far I can tell so far. You don't know when it is closed or open...whimsical. There was a poster I saw in a major train station in Germany in June 2015 prior to the refugee situation, whether you make it political or not, which told of possible situations going to be encountered by DB and train traveling public. . Obviously, not all train poster announcements are translated, (very few are), this one I though should have been: "Mit Behinderungen muss gerechnet werden" (You better count on disruptions). In light of the refugee situation, even more true.
So, you plan for that contingency by having a reserve plan or two, even a back up plan for the back up plan. Main border crossing always affected is that corridor between Munich and Salzburg, with all the factors involved, trains going only up to Freilassing, delayed trains, waiting, busses running between Salzburg and Freilassing, and so. What do you do if you're going to continue with the trip? Plan around it, or be more creative in the choice of routes, ie, use different routes, night trains. limited back tracking, or discount air carriers. In my planning as long as night trains are running, all is not lost in crossing the borders and getting to desired destinations. Use a railway map in planning the trip, more choices.