This story from the Salt Lake Tribune talks about the policy confision and questions surrounding recounts for electronic voting machines in Utah after last month's primary election. While there is some chaos right now, I'm confident that it's going to all get worked out because the proper levers are in place.
Utah's law requires a paper ballot and designates it the "official" ballot. Based on that law, there will be some court challenges and lawsuits and precedent will be established. That's how these sorts of things get worked out.
Some will decry this as messy and expensive, but that's the way democracy works most of the time.