If they had received your initial application before deadline and requested you to re-submit it after correction, They must have also told to do so between certain time limit.. they must have said "we must receive it before certain date". If thats not the case you should've resubmitted the entire application enclosed the letter they had sent you. This matter can be handled better by an experienced immigration attorney and if you don't wanna spend on attorney, Write them a letter explaining the situation and request to kindly re-consider your application because it was actually initially filed before the deadline. Hope this helps!