Using SAM-BA to upload a sketch.bin

I believe I have managed to upload a compiled sketch to a Due using SAM-BA 2.16 GUI.
The sequence which seemed to work was to upload, then run the "boot from flash" script followed by "select flash0 for boot".

The only problem is, I had to erase using the button on the Due before it would see it as a Bossa Programming port, once programmed it sees it as a Due and won't connect.
Are there any workarounds for this?