Missing form 6765

The state told us they're not allowing R&D deduction until we send a copy of form 6765. I went to our long time filed federal return and found that it doesn't have the form even though it does have form 3800 with the correct number on the line I, part 3.

So, Turbotax somehow prepared and filed an incomplete return. Are we screwed?
Based on this IRS article, even if we fine an amended return, it appears you can't go section 280C election, which is what we did when we prepared the return.