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I'm confused by your description. The partition that is shared over USB is not the boot partition. It can be restored by reinstalling the firmware. If you download and copy the firmware to an SD card and reboot the device with the card inserted, I think it would still detect it and install it.
If you can get into the Maintenance menu, then you can also reformat the internal memory that way, too. That will copy back the necessary files that were deleted.
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