Hello there, D_Weavers.

Applying auto credits to an invoice in the project center is not possible. 

However, if you wish to auto-apply a credit to an invoice to your customer, you can do it but not on the project center. 

You just need to make sure that the Automatically apply credits feature in QuickBooks Online is turned on. You can follow the steps above given by my colleague MaryLandT to check if the auto applies credit is turned on.

Also, you can use this article if you wanted to apply for delayed credits. Just follow steps 1 and 2 at the bottom part. Create and apply delayed credit in QBO.

Please leave a comment below if you have any other questions. Take care.