Absolutely, the code in question is part of the Nios II architecture specific code in the kernel source tree.
I can't remember the exact location but we can get that for you if you're having difficulty locating it.
The kernel source code can be found in:
$KERNEL_PLUGIN/linux-2.6.x
After modifying the code, you will need to rebuild your kernel via the IDE.
HINT: If your hardware hasn't changed and you wish to speed up compile time, you can change the
project/build/include/nios2_system.h
file to read only. That'll prevent it from being re-built and consequently, it should speed up the build time. (If your hardware does change, you'll have to switch the file back to writeable so that it can be re-built...)
The above hint won't be necessary in the next release of the Nios II Linux Distribution.