I have some prior experience with this (child of director died) - CRO waived the late fee but not the audit exemption - said that they were statutorily barred from doing this
The CRO wont waive the audit exemption, but if you send in a letter explaining why you missed the due date, they should waive the late fee. A director friend was diagnosed with cancer and missed the deadline and as DB74 mentioned above we sent in letters from doctors etc and we were told they cant do any thing about the exemption as its law.
I had a case 2 years ago where the document was filed on CORE on time by another accountant but was not submitted signed on time. I had to present in person and they accepted it. No loss of exemption. I don't know what was in the note as that was sealed but it couldn't have been anything too serious.