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I think there are times when commented code can be useful, although with source control there is really no need unless you want to preserve an idea in the spot for later consideration.

The issue is that you need to have some good regression testing in place so that situations like the author's don't happen (yeah, right, life is perfect, right?).

That being said, removing code is ALWAYS a pain. Let's be honest, checking for references for every little piece you remove is not realistic. the compiler might catch most of the issues but the bottom line is there is always a risk anytime you introduce changes.