dfu-util should work - but you'd have to use the right firmware file. Did you use the one from http://www.espruino.com/Download or one of the 'cutting edge' travis ones?
The travis builds don't actually contain a bootloader (the file is just padded with 0s), so if you'd uploaded one of them it wouldn't have worked - could that be the issue?
Also with the graphite: all it does is make BTN0 switch to the chip's DFU bootloader rather than Espruino's - so if you leave the graphite on then Espruino should still work. The only issue will be that you'll be unable to enter the bootloader that the Web IDE can use (the one that flashes the LEDs).
Hope that helps!
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