FDA released a draft eCTD Technical Conformance Guide!

Here are some of the main points of the guide:

Transitioning to eCTD

Do not resubmit documents already submitted in paper or other electronic format. Provide only new or changed information.
You should not include the eCTD section number in the leaf title.
For documents of the same type (such as the cover letter, Form FDA 356h, and annual report documents), you should provide additional information in the eCTD leaf title so reviewers can distinguish documents submitted in different sequences. For example, the leaf title for a cover letter should also include the date (e.g., 2015-12-31).
If documents of the same type are being provided in different file formats, a file format (e.g., “MS Word”) should be included at the end of the leaf title.

Presubmissions

Any information submitted in eCTD format before the “original-application” should be coded as "presubmission" and should use sequence 0001. The original application will use the next available sequence number depending on the number of submitted “presubmissions.”
Signed FDA forms are not required for presubmissions. If you are going to submit using the Electronic Submission Gateway (ESG), include a completed fillable form without a signature. Fillable forms aid automated processing.
For INDs, the serial number field can be left blank for presubmissions and should be used only starting with the original application.
There is no requirement for the IND serial number and the eCTD sequence number to match.

Cover Letters

Technical description of the submission, including the approximate size of the submission (e.g., 2 gigabytes), the format used for transmission (ESG or physical electronic media), and the type and number of electronic media used (e.g., USB drive or two DVDs), if applicable
A regulatory and technical point of contact for the submission, including email address

Study Reports

For reports without a file tag, “study-report-body” can be applied as the file tag, with clear leaf title indicating content of the document.
If a document has been provided in a previous submission (e.g., protocol), provide only an eCTD leaf reference to the protocol in the eCTD backbone file, rather than resubmitting the protocol file.

Case Report Forms (CRFs)

FDA does not use the eCTD heading 5.3.7 for CRFs, therefore do not place files under this heading.

IND Safety Reports

Each individual IND safety report with its associated study should be provided in section 5.3 of the eCTD.
Each safety report should be referenced in the study’s STF using the ‘safetyreport’ file tag, with "Safety Report" in the eCTD leaf title along with "initial" or "follow-up," depending on the content of the individual safety report.
Each IND safety report should be submitted as “new” without replacing any previously submitted information. Leaf titles that clearly relate to the individual cases should be used.

Issues and Solutions

Issue: Combining Multiple 3.2.S or 3.2.P Sections With Similar Metadata

This issue is caused by leafs being submitted with incorrect metadata (‘name’, ‘manufacturer’, and/or ‘dosage form’ which are not an exact match to what was submitted previously).

Resolution

Use the eCTD “delete” operator to delete all the leaf IDs that were referenced in the section to be deleted. Deleting all leafs will remove the entire section from our review tool.
Re-reference the existing files using new leaf IDs, ensuring that the ‘name’, ‘manufacturer’, and/or ‘dosage form’ metadata is an exact match to the section where you want to re-add the leafs.
This issue is also caused when multiple 3.2.P sections were submitted for multiple strengths of the same drug product.
In general, when a single application for multiple strengths can be submitted, information for each of the product presentations and manufacturing schemes should be combined and presented together in one Drug Product section, with information for each of the product presentations and manufacturing schemes provided in the Appendices and Regional Information sections, as warranted.

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