In my experience from a neighbouring field, window in this sense is generally translated to Fenster in German, which is confirmed, e.g., by the German Wikipedia article on Fensterfunktion.
Going from what a one-minute Internet search told me about the method, I would strongly prefer wechseln over tauschen, since the latter implies that both windows are used all the time, but only their place of usage is changed when the Tauschen happens. In this context, I would consider the difference between wechseln and tauschen equivalent to that between the English to switch (or to change) and to swap.
However, going by my one-minute Internet research, I would also use a totally different approach to describe the method, namely something along the lines of adaptive Fensterwahl or Fensteradaption, since the essence of the method is not the changing of windows per se, but adapting them to the situation (theoretically, the window could not change at all when this method is applied, in the unlikely case that one window is the best choice for all the data – in this case no window is switched, but its still adaptive).
After I wrote those lines, I did a little more research and found that the technique in question was originally published by a German in German in a paper titled Codierung von Audiosignalen mit überlappender Transformation und adaptiven Fensterfunktionen.