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Can I allocate 9 months of income and expenses to one shareholder and then allocate 3 months of income and expenses to 2 new shareholders on the form 1120S?

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Level 1
 
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Level 15
Sure you can.

ex-AllStar
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Level 8

Start with the Schedule K-1 worksheet enter #of shares beginning of year/end of year.    If you're doing the actual income for 9 months/3 months ProSeries doesn't have a method for entering this information.  It will do a Weighted Average.