Hi Samuel:

If the client account is in negative, you can do a WriteOff batch creating a Payables check batch to miscellaneous vendor or specific vendor if you have it.
When you post the adjustment, it will show up in payables and you change the manual check batch not to print the cheque.

Or, you can just do an adjustment to the customer transaction with a clearing account and create and post a manual cheque in Payables using the same clearing account.
The AP cheque is going to create the BR transaction for reconciliation.