I haven't tested this since I don't have my Harmony with me right now, but judging by usbmon logs for the 5xx upgrade issue, libconcord is sending broken protocol right now. I have no idea if the remote is honoring the length flag in the WRITE_FLASH command, or if the length in the WRITE_FLASH_DATA overrides this. In turn, this might make small writes trash data following what's supposed to be written...
Checkin comment: Fix WriteFlash to send the correct length fields for WRITE_FLASH_DATA.
.writeflash-lengths.patch.swp
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