For us when we have paid email subscribers filling out one of our forms to opt-in to our RSS Newsfeeds or other product trial subscription, we contact the lead and ask which one they should use to receive their email. They're ok with us using only one, but we keep the other email as a secondary email, just in case the other email becomes invalid. Then we merge the records.
If we can't reach them by phone, we send them an email. But if we can't reach them, the email address that receives the paid subscription emails usually the company email, will be the email address that we retain.