Working with Multiple QSF files

The issue appears to be with using specific commands in the pre-flow script in addition to multiple QSF files. I tried modifying the a5gt_golden_top design for FPGA2 provided in the Arria V GT Development Kit SDK. If I move some of the QSF assignments to a separate file and add "source separate_file.qsf" to a5gt_golden_top.qsf, everything works as billed in the documentation. cool. However, if I add a pre-flow script that removes all source code, I get the error message saying that the QSF file has errors. I'll illustrate.

Working pre-flow script:

project_open a5gt_golden_top.qpf
set_global_assignment -name VERILOG_FILE a5gt_golden_top.v
export_assignments
project_close

Failing pre-flow script:

project_open a5gt_golden_top.qpf
remove_all_global_assignments -name VERILOG_FILE
set_global_assignment -name VERILOG_FILE a5gt_golden_top.v
export_assignments
project_close

I've tried a variety of permutations with the code in this script, and the only thing that matters is if I remove all source code. I'm feeling like this is a bug in the toolchain, but I'm far from an expert on Quartus.