QB Issue Resolution:

Edit the Payments received and apply them to outstanding invoices until there are no more un-applied payments.

To find the unapplied payments, create a custom transaction detail report and filter it for Payment type transactions and for the paid status of unpaid.  Double-click a payment on the report to open it, then apply it, and then when you save it, it will disappear from the report.  Do this until all the payment are applied.

Resolution for Issue 'How to get rid of negative balances on the A/R report with out messing with the books?' available: Yes (Solved).
Source: Intuit Community forum.

How to get rid of negative balances on the A/R report with out messing with the books?: 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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