QB Issue Resolution:

When you have a vendor credit available, you can use it partially. It won’t matter if the amount of purchase is less than the amount returned.

Here’s how you can apply a vendor credit to a bill:

  1. Click the Plus icon (+) at the top.
  2. Select Expense or Check.
  3. In the Choose a payee drop-down, select the vendor name.
  4. On the Add to Check portion, select Add for the outstanding bill and vendor credit.
  5. Hit Save and close.

You can check this article for more information: How do I handle vendor credits and refunds?

Resolution for Issue 'How do I process an invoice “vendors credit” that has a purchase that is less than the amount returned?' available: Yes (Solved).
Source: Intuit Community forum.

How do I process an invoice “vendors credit” that has a purchase that is less than the amount returned?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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