If the Sole prop and the S-Corp (as entities) both issue W-2s for a partial year, I would think that FUTA and SS max wages may be miscalculated.
One option is to respond to the IRS notice with an amended (corrected Q1) 941 with the Scorp EIN, and request that they include Q1 info to the Scorp EIN. Then 940 amounts will agree for the entire year. I would include all the information like the 2553 and a letter from taxpayer or Power of Attorney representative for both the taxpayer and the Scorp as an entity, so that whichever agent receives the package will be able to make the change. Include a copy of the old Q1 941 as well and make sure the Power of Attorney form specifies payroll tax matters & forms.
The other is to prepare 2 sets of W-2s, 940s, as suggested by cp_acwt?