The EFS Contingency filing system is currently limited to "new applications, national stage submissions under 35 U.S.C. 371, requests for reexamination, and certain petitions."
The system should be enhanced to include follow on submissions as well.
If not all types of follow-on submissions, then at least the big ones, such as replies to restriction requirements, non-final office actions, final office actions, and whatever else is a high percentage of follow on filings.
You can fax in follow on submissions, so why can't you e-file them?