[NY State] Refund before Amending Return - I will still get the refund right?

Earlier this year, I filed my normal tax return and it told me NY State would be doing an ~$4500 refund. 

I later realized I made a mistake in some of the calculations / attributions, Upon fixing it and on the IT-203-X form where I see my original refund listed as a overpayment on Line 68, TurboTax recalculated that I now owe $4700. 

As I understand this, the calculation assumes I received a $4500 refund, and need to pay back now $4700 (my net taxes are ~200). However, when I called NY State, they told me they don't see the first refund being processed, they only see the amended return with my payment and that they don't have a refund processing. 

Now I'm trying to figure out if I'm misunderstanding something about this - am I correct that when I submitted my amended return, the $4700 number assumes I received $4500 and that the NY State still owes me $4500?