Due to a problem in the Quartus® II software version 12.1sp1, you may see smart compilation fail with following messages in compilation if the project has .qip file and enables the smart compilation option.
Info (###): Detected changes in Quartus II Settings File (.qsf).
Info (###): Assignment SLD_INFO with value QSYS_NAME test HAS_SOPCINFO 1 GENERATION_ID ### has been deleted.
To work around this problem, use command line for the smart compilation.
quartus_sh --flow compile <your_project_name>
(e.g. quartus_sh --flow compile top )
This issue is scheduled to be fixed in a future release of the Quartus II software.