Due to a limitation in the Quartus® II archiver versions 13.0 and earlier, you may experience problems when archiving and restoring a design if the project Quartus II Settings File (.qsf) sources other .qsf.
For example, problems may occur if your project .qsf contains the following:
source "../data/constraints.qsf"
In this case, if the project is archived and then restored, the file constraints.qsf is restored to <project folder>/data/constraints.qsf.
The project .qsf is not automatically modified to match the new relative location of the constraints.qsf file.
To work around this problem, manually modify the path in the project .qsf to match the new relative location.
This problem is scheduled to be fixed in a future release of the Quartus II software.