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I just had to deal with the same issue, only running cPanel. Nothing would tell me that I had to revoke the old certificate, nor how to, had to deal with what sounded like GoDaddy's version of the old piano lesson staple "The Entertainer" for about 10 minutes to get a hold of their support. Luckily the tech was able to diagnose and fix the issue within 5 minutes of conversation. Bloody Nightmare.