Self-programming issue on CW303 XMEGA Target

I am trying to upload a program that uses the XMEGA Self-programming example where some of the functions need to be located in bootloader section to be able to use the SPM instructions.

I defined in a .BOOT section at address 0x20000(should be the bootloader section of the ATXmega128D4-AU on the XMega target) which in the Makefile is defined as:

LDFLAGS += -Wl,–section-start=.BOOT=0x20000

Problem is, I keep getting the errors linked below and I am not sure why.

Here is a copy of the map file generated map_file - Pastebin.com

Any help is appreciated

The datasheet says that protection level of the boot memory is determined by fuse bits. Have you looked into modifying those?

I completely overlooked that, thanks for bringing that up.
I am going through the chipwhisperer source code and it looks like it includes functionality to overwrite the fuse values but I don’t know where these should be passed to the toolchain.
Any ideas?