The serial console connection does not "time out".
But erasing and re-programming the flash is a very power hungry operation.
The SoC will "reset" and perhaps try to do a "restart" on a low battery voltage alarm.
What you describe reads as if you started the write operation with a less than fully charged battery and now it is to far dis-charged to run the Kindle.
Re-charge the battery!
Note: In this condition, it may take a few days to re-charge while the Kindle is in its "under voltage - safety mode".
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