It would be nice if the IRS was as understanding as that but they aren't. When you file this 1065 it will be seen as filing a return almost a year late. They will almost certainly send you a bill - and a big one.
That is why I say you should gather up the documents you need now - be prepared. Have a copy of the schedule C that shows that the business was reported albeit incorrectly. Then you'll send that form (and your 1040) along with proof that you filed on time and a letter explaining what happened. Since you did file timely that should - no guarantees, but should - get them to abate the penalties.
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