1.(a) Visit to the GST officer with form printout alogwith the documents. Brief him about the situation. Might be he will allow you to overwrite it manually but don't do it on your own.
OR
(b) He will ask you to wait for some time to get the online submitted application lapsed and you will again submit the online application.
2) Submit the copy of LUT form offline along with the docs with the proper officer. Once he will issue you the LUT certificate you are eligible for export without payment of duty. LUT is issued within 3 working days.
Thanks