Once a tax return has been e-filed it cannot be canceled, retrieved or changed.
If you have e-filed your tax return and need to change the information on the tax return then you will need to wait for the tax return to either be accepted or rejected by the IRS.
If the tax return is rejected then you can make your changes and re-file the tax return.
If the tax return is accepted then you will have to amend the tax return to make your changes. An amended tax, Form1040X, return can only be printed, signed, dated and mailed by you to the IRS, it cannot be e-filed. The IRS will take up to 4 months to process the amended tax return.
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.