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Generally, non stock, non standard, third pary modifications to devices will not be handled by calibre. The root you applied is such a case and will not be supported if the device does not interface with calibre properly.
As for the debigging mode causing the device to be detected incorrectly, there is nothing we can do about it. It is an issue with the device firmware you will need to take up with the manufactuer. In that mode the device is identifying itself as another device.
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