Nios II hanging/crashing on PIO write?

Is this a Qsys or SOPC Builder based design? If it's Qsys then perhaps you are writing into space due to a mismatch between the software and hardware (Qsys is less forgiving when it comes to writing into space). I recommend putting the system ID peripheral into your system to help catch some of the mismatches Daixiwen mentioned.

I would also try simulating the design. That should give you more insight into what is causing the issue.

Last but not least, how much space do you have left for the stack and the heap? Could be that you were on the hairy edge of running out and the code change with the new PIO put you over.