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?"
When transitioning to eCTD format, you are not required to resubmit documents already submitted in paper or other electronic format. In general, resubmission of previously submitted content is neither necessary nor recommended.
FDA recommends that you contact the eSubmission (ESUB) team at esub@fda.hhs.gov when converting to eCTD format for specific advice and help, prior to submitting an actual eCTD submission.