You should not file an amended return until your first filing has been totally processed (you get your refund)
It is not mandatory to file a 1098-E. So, you are not required to amend. But, form 1099-E is for student loan interest, which is an "above the line" deduction. You don't have to itemize to get the deduction.
So, unless your tax was already at 0 or your income is too high to qualify for the deduction, there should be some benefit in filing an amended return.
