I first prepared the MFJ federal return and submitted the E-file earlier today using the Premier Download software, and it got accepted after half an hour. Since my husband and I lived in different states last year, so I prepared my own NY state e-file in the software (using the mock-federal method from the FAQ: I changed my status to MFS and removed the income and deduction amounts that come from my spouse). HOWEVER, after I reviewed everything and submitted only the NY state return successfully, I found that the printout records show that I filed my federal tax again together with my NY state return! Of course the refund amount is different from my previous filed MFJ amount.
This is so odd and confusing!!! I remember when I was reviewing my NY state return in the final steps, it recognized and showed me that my federal return was already transmitted, how would I know that it would be filed again with my state tax??
I'm so confused and not sure if my return would be rejected.