I received 2 W-2’s from my workplace (Amazon) but when I enter the second W-2 my estimated return decreases ?

Yes that is common.  But why did you get 2 W2 from Amazon?

You only get one refund or tax due for all your income combined.  The more total income you make you pay a higher percent for tax.  And each W2 was withholding like it was your only W2.  

Did the two W-2's from Amazon have something to do with Amazon changing their payroll service or the payroll periods?   I have seen a few of these where Amazon issued two W-2's to the employee.