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As long as the return is prepared correctly and as long as the 1120S was prepared correctly, there is noting to sweat - life is good.
This also sounds like you might have an NOL (Net Operating Loss). You need to carefully consider making an election to NOT carry the loss back, or maybe you do want to carry it back to prior years.
Here is a little light reading to get you started. https://www.irs.gov/publications/p536
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