I don't think this is a Duet problem, it's the drive itself going to sleep.
What kind of drive is it? Some drive manufacturers have a utility program or procedure to flip off the sleep mode built into most drives these days, it's a power saving feature. Sadly, not all drive makers have made it possible to bypass the sleep mode.
Jump on the Tech support forum for the drive maker, someone there has surely asked this question.
Note that often third party companies like LaCie will make a drive using someone else's drive like Western Digital.
You can set the step pulse parameter using the T parameter in the M569 command. You don't need to change the pulse width when using the drivers that are built-in to the Duet, but you do need to when using most types of external driver.
It's hard to know whether it's just the CPU that's been damaged, or other components too. If the blue LED on the WiFi module turns on as soon as you apply power and stays on, then it's likely that at least the WiFi module is damaged too.
It's a long shot, but you could try erasing the firmware, by fitting the Erase jumper and applying USB power for a few seconds. Then remove the jumper, connect to a PC via USB again, and see whether the Bossa port appears.