late 5500 filed, extension not recognized

[Santo Gold]

We have a 401k plan with a 3/31 PYE.  We filed a 5558 before 10/31, completed the 5500, which was filed around 12/20.

However, the IRS sent a letter stating that the 5558 was received late and therefore was rejected.  The 5558 was not mailed with tracking and not filed electronically.

Just curious as to whether the plan sponsor has any options here.  They already filed, apparently late, but that has not yet been "caught" or addressed by the IRS.  Can they file via DFVCP, pay the fine, and put this behind them?  But is DFVCP available if they are already filed?  

Thanks for any replies