Regarding the self employment tax deferral, we have entered the se income into line 18 of schedule SE part III and it is calculating the amount available for deferral on line 25 as $8537. However, It is not reducing the SE tax or transferring the amount to Schedule 3 as a prescribed by the instructions. Is there a checkbox or something to allow the SE tax deferral?
Have you looked at the worksheet for Line 12e of Schedule 3 (look on the "1040 Wks").
The law says you can't get a refund of amounts already paid; you can just defer unpaid amounts (although I personally think the way IRS set up the worksheet is questionable, and it could possibly be argued to get a refund in many cases).