Due to a problem in Quartus® Prime Pro Edition Software version 23.4 and earlier, rather than just allowing you to rerun the assembler, the Quartus® GUI will force a recompile when changing any security settings in a precompiled project when using Stratix® 10 or Agilex™ 7 devices.
You can avoid this full recompilation by selectively running the assembler from command shell (quartus_asm) to generate the .SOF with updated security settings.
This issue has been fixed starting from Quartus® Prime Pro Edition Software version 24.1.