Your questions are making me wonder if you amended from a joint return to separate returns correctly. Did you follow the instructions in this link? And did you use Form 1040X for each of you?
https://ttlc.intuit.com/questions/2895311-how-do-i-switch-from-filing-jointly-to-filing-separately
And when you prepared those separate returns did you follow the strict rules about both of you itemizing or both of you using standard deduction? It cannot be one of each. You both have to file the same way.
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