Firstly, examine your own motivations. I find that 95% of people who tell other people they're doing it wrong claim it's for the "good of the company" but really just enjoy feeling better than other people. This is why they fail at ever making friends or convincing people, because they are unwilling to give the advice unless they make themselves the larger person in the process.
If you want to help this one individual, and your motivations are pure, then befriend the individual, and after a few hours see if you can find a way for them to solve it on their own by offering yourself as a sounding board. If done right, they won't realize the degree to which you helped them.
But if you're afraid of over-a-year's worth of time being wasted, it sounds like the larger issue is how inefficient your company is. I'd either make peace with that or try to solve the problem at its root.