Good day to you, D_Weavers,

Someone may have accidentally disable the Automatically apply credits feature in QuickBooks Online (QBO). That's why credits aren't applying anymore.

You'll want to enable this feature by following the steps shown below:

1. Go to Settings ⚙, then select Account and Settings.
2. Click Advanced tab, then select Edit ✎ in the Automation section.
3. Select Automatically apply credits.
   
4. Click Save, then Done.

After that, you'll want manually apply the credits first. Moving forward, QBO will then perform this process for you.

Feel free to read through this articles: Create and apply credit memos or delayed credits in QuickBooks Online. It has detailed steps and screenshots for your guidance.

Also, you can use the Audit Log feature to know who made the changes in the system. This records all activities in your account.

Let me know if there's anything else you need. I'm always right here to help.