You may see this error in the Quartus® II software versions 13.0 and earlier when compiling a design containing design partitions that were created using the Design Partitions Window.
For example, this problem can occur if you create a design partition in the Design Partitions Window either by clicking the <<new>> cell or by right clicking and selecting Create New Design Partition. In this case, the Compilation Hierarchy Path, the level of hierarchy specified for the design partiton, is incorrect and is not recognized during subsequent compilations.
To work around this issue, create your design partitions by selecting the specific entity from the Project Navigator Hierarchy tab and then right-clicking, pointing to Design Partition and selecting Set as Design Partition.
This problem is scheduled to be fixed in a future release of the Quartus II software.