Was it a S Corp stock sale  or asset sale? 

If stock sale and If the buyers and sellers agree to this - you file one tax return with the income/expenses allocated based on actual amounts for the actual time period owned.   Must make an Sec1377 election on the return.  Enter Date of Changes in Ownership on SmartWorksheet.  ProsSeries does not have a worksheet for calculating the correct amounts per shareholder  - you will have to override the K1s.

I had SCorp that had a stock sale twice in one year. I used P&Ls to get the correct information on return and correct amounts per each shareholder.  Takes some time but it can be done.

Option 2 for a stock sale is to prorate the year to date totals by ownership percentage.  Enter Date of Changes in Ownership on SmartWorksheet.  ProSeries will (should) do the calculations.