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You should get a W-2 for when you were an employee and a 1099MISC for when self-employed. 

Unless you stayed an employee, and after Jan. you just had no taxes deducted, then they would issue one W-2 for the entire time. 

If social security was taken out of the pay in Jan, then you should get two W-2's.  Because the 2nd W-2 (with no Social Security Paid) you will  get a screen after the W-2 enter that should be checked "Religious Employment".

This screen is titled, "Do any of these uncommon situations apply to this W-2?

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