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When someone updates or changes something in the Account and Settings page, the Settings changed status will be reflected in the Audit Log. You can see it in the Event column and it also provides you the name of the user and the date changed.
For more details about using the Audit Log feature, check out these articles:
On the other hand, I've checked here on our end and there's no reported case about this one where the Automatically apply credits feature is not working. To better isolate if this is a browser issue or not, let's access QuickBooks Online (QBO) using a private or incognito window.
Here's how:
Then, check if the credit automatically applies to the next invoice you create for the same customer.
If it works, try clearing your browser's cache to delete those temporarily stored files. You can also use other supported, up-to-date browsers to be thorough.
I've got a link here that provides you with articles about managing your customer transactions: https://quickbooks.intuit.com/learn-support/en-us/sales-and-customers/07?product=QuickBooks%20Online.
Keep me posted if you need a hand with creating recurring transactions or any QBO related. I'll be here to help. Have a great day ahead.