After you file

....and then it wiped the "Total refund amount" at the top and replaced it with the 2nd tax return. Then I continued and E-Filed with the 2nd one only.

 

No both W2s should still be on your return.  Check 1040 line 1 for the total wages.  You probably saw the refund refund reduce.  That is common. It just looks that way because you put them in as separate W2s and saw the tax due change in between them. If it was all on one W2 you would get the same result. And each job was withholding like it was your only job.


Because you only get one standard deduction no matter how many W2s you enter. Turbo Tax starts out by giving you the Standard Deduction. You entered more income when you entered the second W2 but you didn’t enter more deductions. And each job only withheld taxes like it was our only job for the year. You might want to adjust your withholding. Also as you add more income you might not be getting as many credits as before like the EIC credit.