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Hi justforfun,
when a new code is uploaded through OTA it is stored in the SD with the name you gave it. If you do not repeat the same name for a new program, all of them will be stored in the card (take into account that if you want to keep your original code uploaded to the mote through the USB stored you will have to store it manually or upload it again through OTA).
Regarding your discovery problem, the most likely possibility is a mismatch in the XBee configuration. Could you please check that the information in the xbee.cong file corresponds to your modules network configuration?
Regards.
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