Hello Andrew,
Thanks for your question. I've tested this and I've basically reached the same point.
I'd suggest you to rather switch the symbol files via "Debugger Console" / GDB client console as a workaround.
e.g. to load bootloader symbols type the command below into GDB client console:
symbol-file <Path_to_your_BL_elf>\S32K144_bootloader.elf -readnow

* refresh the IDE (menu File ->

and now the bootloader sources/symbols are available:

repeat the steps for the application symbol-file:

In the meantime I'll check with our debugger team what might be wrong with add-symbol-file.
Regards,
Stan