We would change the account to Mary's name/SSN. Since she was a joint owner, she earned the interest the same as John did--the account was simply set up with John as primary, but it could just as easily been the other way around. The account earned the same interest, regardless of which owner was listed as primary. But, if Mary had been added to the account later than the beginning of the year, I could see where you might have a need for different 1099s.
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Newbie Mgr