Have a look in the code, the GPU is most probably using that file to turn on/off interrupts, if so that is an easy fix. Although the screen may use interrupts ( couldn't download source, their website isn't chrome compatible, or there is a lot of stuff missing ).
int types can be changed in code to their constant sized equivalents, I.e.
uint8_t = 'unsigned char'
int16_t = 'signed int'
Or you could create some typedef's that you can replace some types with and then if you need to change, only the typedef needs fixing.
Post the .h and .cpp if you can't manage to fix it. I'm not Due savvy, but I can help you remove the AVR stuff which you can go find replacements for.