After you file

How did you amend?  What order did you do things? You said you updated your return, then you amended?  No.  You have to amend by starting with the first original return.  So did you take out the changes you made when you updated before amending?

 

Also when you amend it assumes you got the first original 6,000 refund.  So you have to change that to zero on the amended return.