The following error may occur when running the EDA Netlist Writer in the Quartus® II software version 5.0 when the project contains Preserve Hierarchical Boundary assignments and one of the Incremental compilation options is selected.
This internal error has been fixed beginning with the Quartus II software version 5.1.
The Preserve Hierarchical Boundary assignment preserves hierarchical boundaries throughout compilation during the regular compilation flow, but these boundaries are not preserved through fitting in the incremental compilation flow. Altera® recommends that you do not use the Preserve Hierarchical Boundary assignment together with incremental synthesis or full incremental compilation. To work around the problem in version 5.0, remove one of the two types of assignments.