After you file

"Her" federal  "our" return.

Did she file Married Separately, and then amended to Married Joint?   When doing a 1040X amended return, the refund meter resets to zero.  Then only any changes are shown.  Amended returns must be filed by mail. After 3-4 weeks, you can start checking here:

https://www.irs.gov/filing/wheres-my-amended-return

Please explain exactly what she/you did.