This warning message occurs in the Quartus® II software when you use the bottom-up incremental compilation flow to compile a project that includes an imported lower-level Nios® II design partition or other encrypted Intellectual Property (IP). The Quartus II software does not generate programming files if you compile a design with an imported design partion that includes an encrypted design (such as the Nios II processor).
For instructions to work around this issue, refer to the Quartus II Incremental Compilation for Hierarchical & Team-Based Design (PDF) chapter in volume 1 of the Quartus II Handbook.