Level 15

What was he doing when he was filing Schedule C?  Was he working for some companies that considered him an independent contractor, and others that told him sorry, but he's still an employee?  Then the companies that issued him a 1099 for non-employee compensation should now issue the 1099 to his LLC/S Corp (if any 1099 is required) and the companies that consider him an employee should continue issuing him a W-2.

Your job, if you choose to accept it, is to separate the expenses attributable to the S-Corp income (which are deductible on the 1120-S) from the expenses attributable to the employment income (which were flushed away by the 2017 tax legislation).