Due to a problem in Quartus® II software version 13.1 and earlier, you may see the HDL Design file is not generated from a Block Design File (.bdf) file when you select File > Create / Update > Create HDL Design File from Current File. This problem occurs when the .bdf is not stored on the same drive as the project directory.
To work around this problem, place the .bdf in the same drive as project directory.
This problem is scheduled to be fixed in a future release of the Quartus II software.