Rolling back removes certain files so they don't conflict with new ones you want to install. When you restart Commander everything is 'Unrolled'. When you finish a game, the newer versions of Commander will ask you if you want to rollback. Just click yes. The very newest versions actually have an 'Auto-Rollback' function you can enable.
As for which options, Jim has the answer. I play with malfunctions but no sabotage. Each one tells you what it does, so it's pretty easy to decide what you want.
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“Never do anything you can't take back.”
—Rocky Russo
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