@mcbeth628 lesson learned: do not file an amendment until the original return has been processed. Obviously, the IRS processed the original return and is not aware of the amendment. They caught the error you caught and adjusted accordingly.
I am having trouble following the math
When you created the amendment, how much did you pay?
how did you pay the $2623? by check? at the irs portal?
when did the payment clear your bank account? (date)?
can you see the $5600 charge on your transcript?
you will probably get a letter shortly demanding the remaining money. there is a section explaining how to dispute it. I'd wait for that avenue to complain - could be the $5600 posts by then and in effect they owe you - I'd explain that in the dispute response.
