The RESPA Roundup article refers to a total failure to deliver a GFE. We are aware of situations where the examiner has required the a total refund of fees for the failure to deliver the GFE within the required three business day period.
If an examiner orders a refund of excess fees they will expect you to go back to the date of their last examination, just as they do with Truth in Lending reimbursement. Regulation X provides that a violation may be cured at closing or within 30 days after closing. Beyond the 30 day period refunding fees to the customer does not cure the violation; you still have legal liability. But refunding the excess fees will likely appease the examiner.
This issue is not addressed in Regulation X or the Frequently Asked Questions.