Are you trying to accelerate something that pulls in the CFI flash drivers? If you are looking to improve computational performance I would look for something else to accelerate besides flash accesses.
To debug this I would first switch to the software only implementation and make sure that compiles properly first.
I just went to line 82 in that file and found a struct. Take a look at the C2H user guide and near the end you'll see what the tool doesn't support (pg 113/118) here:
http://www.altera.com/literature/ug/ug_nio...2h_compiler.pdf (
http://www.altera.com/literature/ug/ug_nios2_c2h_compiler.pdf)
I hope that helps