Agree the article is very vague on what he was doing when filing. Most likely he was not paying the self-employment taxes and get audited; however, like you said, he should have been deducting expenses. I am not an accountant or tax attorney, but I believe in this case, as long as he kept detailed records he can go back and refile. They may ask him for receipts and documentation, but that should be fairly easy to acquire from his hosting company. I have had to refile my tax return for a previous year, it was not part of an audit, just missed a 1099 and didn't realize it until the following year. My accountant took care of refiling and ended up getting a larger refund.