Your assignments may not be imported into your project if the top level entity in the QSF does not match the top level entity of the current project.
Assignments stored in a QSF are successfully imported into the current project if the top level entity of the current project matches the top level entity name in the QSF, or if Analysis & Elaboration has not been performed.
To import the assignments in your QSF, change the top level entity name in the following QSF entry to match the entity name of your current project:
set_global_assignment -name TOP_LEVEL_ENTITY <current top level entity>
Beginning in the Quartus II software version 6.0, assignments not related to the entity can be imported without the above TOP_LEVEL_ENTITY assigment. The software issues a warning message if an assignment can not be imported.