Nope, rollback and recopying the files won't hurt anything.
Ummm.. 12 hours straight in fine weather in NYGM will still result in your crew being nearly exhausted I believe.
I've read in a few places that it's ok, no problem because an exhausted crew works just as hard as a fresh crew. So I tried that the other night.. i finally got the message "not enough people in the engine room" and my ship stopped. So obviously that's incorrect.
I've tried setting the 3D view down and using the "trick" of high TC to keep your crew static till battle. While it works for a while, eventually you'll end up with two sets of mostly exhausted crews and it's a nightmare trying to rest some while the other work, but not too hard and blah blah. It's almost easier (buy far too many clickdrags) to just use the 8 hour shifts.
8 hour shift rotations means a painful amount of clicking and dragging, but you've always got a rested crew on duty and a partially rested crew in reserve in case things go wrong.
I set up two crews for each compartment, then three watch crews. At 0800, 1600 and 0000 I swap in one of the three watch crews and rotate everyone else. Just wish there was an easier way of doing that.