If you filed and received a tax refund last month, you cannot e-file again. The return will be rejected. You only file 1 tax return per year, so you will need to file an amended tax return when you get a copy of your other W-2. You have 3 years to file the amended return. If you can't get the copy, you can contact SSA to get a wage report or wait for the IRS to send you a notice.
Generally, you do not get your social security and medicare taxes refunded; you only get the excess income taxes that were withheld. And if you only filed one of your W-2s, you will likely owe income tax when you amend the return since you only get one standard deduction and that was used when you filed your original return. If you wait for the IRS to send you a notice and you owe tax, they will charge you interest so it will save you $$ if you get the return amended sooner than later. @saran_1994
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