bossac.exe --port=COM7 -U false -e -w -v -b Blink.cpp.bin -R
you need to add the location of the bossac.exe (somewhere inside the arduino folder) to your path file
Every time I need to re-load a sketch in the Arduino Due using bossac as you mentioned, I have to erase-reset the board. Why?
I don't know yet. That is not happening with Arduino IDE. I have checked this phenomenon with Windows 7 and Windows XP with same results.
May be Arduino IDE shows in the verbose output, just part of the enumeration of the upload.