While amending 2020 state taxes the amount I owed disappeared incorrectly

I was amending my taxes and  after all info was updated, Turbotax initially had that I owed $ back which I do, but then it disappeared and now says I owe $0. The rep at Turtbotax was baffled. She said it looked like I already filed the amendment, which I clearly didn't (it needs to be filed by paper and no records of another amendment). 

Has anyone had this happen?  I was told to just submit the amount I owe even thought he state 1040X says I do not owe anything.. I'm not totally comfortable with this work around.

Any help or advice would be so greatly appreciated! 

I should add I have not yet received the refund that I will owe back. 

Thank you!