I'm pretty sure that is because of what I said earlier: http://forum.espruino.com/conversations/297591/#13376991
I just tried this and it's easily fixed by typing reset(). I guess the IDE could just manually send a reset after E.setBootCode() to make it less likely you hit this.
The thing @stevie4711 has is different though - it can't be recovered with reset() or any normal commands.
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