Are there any drawbacks to trying to use the SAMD core bundled SDU library with the MKR GSM 1400?
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It takes 16 kB of flash to use the SDU library, there's a secondary boot phase added after the boot loader to check the SD card for the update file.
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If the update becomes corrupt or invalid, you'll need physical address to recover it via sketch upload over USB. You could use SHA256 or CRC etc, to validate the downloaded file before applying the update to avoid corruption during transport or storage.