You are correct, his last medical certification is the one that matters. So, to get a new one today, even 3 years later, he would have to answer all the questions honestly including that he has had a medical certificate for less than 2 years. If, when the evals are done and the long form was filled out the same as the previous one (except for anything that has changed in the last 3 years) the new certified medical examiner finds he does not require a sleep study the certification is valid and will hold up to FMCSA scrutiny.
Getting a second opinion is not a bad idea, the only requirement FMCSA has is to compare apples to apples, meaning answer the long form questions exactly the same for both examiners.