Description
When loading an existing custom peripheral into the Qsys component editor, only the top level HDL file is displayed in the GUI. On saving the peripheral, all other source files are lost from the generated _hw.tcl peripheral file.
Resolution
This is a current known issue in the Quartus® II 12.0 Qsys tool, and shall be fixed in a later version. The user will need to add the other required files into the component GUI before saving, or alternatively make edits to the peripheral using a text editor.