i think i have found the way to do the building with no files swapped needed in the toolchain and all the modules firmware should build correctly.
I was doing comparison of of the installed avr32 toolchain folder(older version, v3.4.2.1573) with and the most current version on atmel site(v3.4.3.22)
theres were differences in the number of folders and files(between the old and latest toolchain) and certain files which are needed to build the hex file are missing from the latest version of the avr32 toolchain.
some pics to show the differences, left side is the older version toolchain folder and and right is the latest installed version.
1st pic- comparison of the main installed folders
2nd pic- comparison of the header files folder in which the latest version tool chain in missing an avr32 folder(which should contain the actual header files)
3rd pic- comparison of the bin folder which should have a “make.exe” file needed to build the firmware
in short, the older toolchain seem to be working over the latest one,