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Yes, you're right QuickBooks only allows the same job in applying for credits and doesn't apply for a different job.
To make sure that it was applied correctly, you can delete and recreate the credit memo and manually apply it to your invoice. Let me walk you through the steps on how to do it:
To delete the credit memo
To recreate the credit memo
Also, you can uncheck the Automatically apply payments so the credit will not apply to other open invoices. Here's how:
For more details, just click this article: Give your customer a credit or refund in QuickBooks Desktop for Windows.
On the other hand, you can also check this link for your future reference about QuickBooks Desktop and how to resolve issues when applying a payment:
Reach back out to me if there's anything else you need concerning QuickBooks. I'm always here to lend a helping hand.