Change NIOS Hardware Get Makefile ERROR

I have a small NIOS 2 system, some VHDL code and just the Hello World software. Every time I change the VHDL code and re synthesize I also do a BSP rebuild specifically adding a SignalTap core or changing that core. I still get a makefile error 1. The only way to get rid of the error is to delete the "software" directory or start a new project. How can this be prevented? What am I doing wrong? I thought by rebuilding the BSP that is should work. It doesn't. Thanks, swimteam