SOPC Builder .qip file is missing all the HDL source files

For anyone else experiencing this problem, I ended up working around it by writing a TCL script that generates the appropriate assignments from the PTF when the QIP is loaded

proc util_qip_from_ptf {filepath} {
  set fp 
  lappend map __PROJECT_DIRECTORY__ 
  while { >= 0} {
    if {*Synthesis_HDL_Files = "(.*)";$} $line {\1} line]} {
      foreach hdl_file  {
        set hdl_file ]
        if { ".vhd"]} {
          set setting_name VHDL_FILE
        } elseif { ".v"]} {
          set setting_name VERILOG_FILE
        } else {
          puts "Ignoring unknown HDL file type: $hdl_file"
          continue
        }
        set_global_assignment -name $setting_name $hdl_file
      }
    }
  }
}

set_global_assignment -name IP_TOOL_NAME "Fake QIP File"
set_global_assignment -name IP_TOOL_VERSION "1.0"
source 
util_qip_from_ptf