The C2H Compiler does not support multiple build configurations (e.g. Release or Debug) in the Nios® II IDE. After creating one or more accelerators in a particular configuration, the C2H Compiler produces undefined results if you switch to a different build configurations and create more accelerators.
To workaround the issue for a specific SOPC Builder system and Nios II IDE project, specify the same C2H settings in both build configurations. Note while switching between configuration you may inadvertantly regenerate the SOPC Builder system or cause a Quartus II recompilation.