You do not need to file a separate return and even if you tried her name and social is still on your return and probably would be rejected. As you surmise likely the IRS system has not caught up with the social security changes. If you are expecting a refund I suggest you go ahead and file using the print/mail option to file the joint return.
If you are expecting to owe a tax you might wait longer and try the e-file later and if necessary print/mail the joint return later in the season (18 Apr deadline).
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