Turning off a pc does not hurt it, and actually prolongs the life of the hard drive motor, not that you'll ever wear it out in your lifetime, and actually turning it off clears some of the cache. If that were the case, then every electronic device you own would be failing. Now on to the ecu. lol
Disconnecting the power will prob have the same affect as disconnecting the battery on your car and will reset it to factory settings. A ecu learns over time.
If it's a non fuel injected ski, then there's no issue, and no harm.