I would complete a Reasonable Cause Letter and attach it to the 5500 filing. The IRS is pretty understanding when an extension was missed, if you have a good reason and can make a statement as to how the extensions will be handled going forward so this doesn't happen again. It also makes a difference if the plan has a track record of always filing on time. You can always call the IRS and ask them this question, without a need to tell the IRS the plan in question. I have used a Reasonable Cause Letter in the past a few times for different issues that have occurred and they were always willing to waive the penalties.
