How to execute NIOS II Command Shell commands from a *.bat file

You'll need to use a different drive mapping than you are accustom to on windows. Something like this might work better:

sh /cygdrive/c/altera/91/nios2eds/test.sh

I would start with something simple like putting your script in the default location that the Nios II command shell opens at and then work in the path later once you have that working first. When you add the paths I recommend not putting the script in the ACDS installation directory since it's a good idea to keep your custom stuff separate.