I just converted the seeedstudio e-paper libraries today.
Basically, you want to put in a header directive to wipe out any PROGMEM commands, and to add the DUE's processor to the if-defines.
Sort of like this:
#if defined(__MSP430_CPU__) || defined(__SAM3X8E__)
#define PROGMEM
#else
#include <avr/pgmspace.h>
#endif
// if more SRAM available (8 kBytes)
#if defined(__AVR_ATmega1280__) || defined(__AVR_ATmega2560__)|| defined(__SAM3X8E__)
#define EPD_ENABLE_EXTRA_SRAM 1
#endif
I have a few more things to work out (such as the refresh rate being horribly slow) and then I'll upload it somewhere for sharing.
PS. Try the image flash sketch; that one worked for me with no changes.