The first question sponsors have when transitioning to eCTD format is, "Do I have to resubmit anything if I've begun the process in non-eCTD format?"
Resubmission of previously submitted information is generally unnecessary when converting to eCTD format.
FDA recommends that you contact the ESUB group at esub@fda.hhs.gov when converting to eCTD format for specific advice and help, prior to submitting an actual eCTD submission.