QB Issue Resolution:

You make an Other Charge type item for prepayments. Link it to income, for a Cash basis entity; link it to Liability, if you are allowed to carry liability.

Use this on a Sales Receipt when you get the prepayment.

Use it later on a Credit Memo for the date you are ready to apply it to the actual invoice, to refund it, or to meet Both Needs. Use the icons at the top of the credit memo.

Resolution for Issue 'How do I record down payments and then later invoice the customer without QB showing a negative accounts receivable balance?' available: Yes (Solved).
Source: Intuit Community forum.

How do I record down payments and then later invoice the customer without QB showing a negative accounts receivable balance?: 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.

Support for actual invoice
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Error Recovery for actual invoice [Canada]
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