If you can get access with the IDE then you should really be ok to upload - but require("Storage").eraseAll() typed on the left hand side will reset everything so you'll definitely be ok.
If you can't access anything at all via the IDE then you may have managed to get it into an odd mode where there's just enough stuff installed to disable Bluetooth, but not enough to re-enable it.
I have just pushed some changes and you should see builds in http://www.espruino.com/binaries/travis/master/ in a moment or two. If you upload that then afterwards holding down BTN1 while starting will ensure that NOTHING is loaded, and you'll definitely be able to connect and re-upload apps.
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