I’ve looked at my tax transcript and I’m seeing a negative balance.

If your IRS tax transcript shows a negative amount that means that that money was owed to you.  Whether it has already been paid to you or not is something only you can answer.  If it is the same amount as the refund that you already received then you already got the money.  If it is more than that then you should contact the IRS to see if there is an amount due to you showing in their system.

@amroskay