"We have a base price for each lot and options are added."
Are you using Estimates for this part, and change orders for the Options?
"The sales
person added a duplicate option after the lot was complete. I informed
them it was incorrect"
Duplicate option? Duplicate of what? How is it incorrect?
"and they insisted it was correct. I added the
additional option to the estimate"
I recommend never changing an estimate; you add this as an Additional Estimate = the additional scope of work. This is especially important if you Progress Invoice from the estimates, as opposed to Time & Materials.
"and created an invoice for the phase.
After they paid us via direct deposit they determined it was an
overpayment."
It isn't an Overpayment. Perhaps you means it is an OverCharge?
"Now they are going to debit our checking. How do I handle
this in QB? Do I enter a line item on the estimate with a negative
amount and create a new invoice with a negative?"
I recommend you stop updating Estimates. Each of these is a New transaction and new activity.
A refund from a Paid condition is done using a Credit Memo. In your case, if the entire additional scope on that invoice is wrong, then list the same info here, by editing the invoice; at the top, create the Credit Memo for Refund. At the top of the Credit Memo is the icon to issue the refund.
You don't do this for an Overpayment. You do this for an OverCharge condition, that is paid in full.