Consider this scenario:
You could use Journal Entries to move the amount of the credit first to a Clearing Account, and then to the second job. However, this requires you to link a Journal Entry to a Credit Memo and that can put your cash basis balance sheet out of balance.
You could issue an Invoice to offset the all or part of the credit memo. This avoids the cash basis balance sheet issue, but the Job Costing reports will be distorted.
When you create the Credit Memo for the first job, the result is an overpayment. The preferred solution is to:
If these steps do not resolve the issue, you can read discussions and post messages and questions relating to your issue on the Intuit QuickBooks Community site for free or you can contact a technical support agent for additional guidance. Fees may apply.