Hello,
But it looks you like you in both cases referring to the same linker file
bootloader's S32K144_64_flash.ld. then I find app's S32K144_64_flash.ld
Do you have 2 separate linkers? If not, then you are modifying the only one which must propagate in both locations you describe.
What are the names of the 2 linker files?
Best regards,
Peter