QB Issue Resolution:

Not really, and they don’t need to be linked. You have them in the opposite sequence, but all you need to do is Close the line items on the SO or close the entire SO, if you know you invoiced it. It is only a planning tool; you don’t need an SO at all, if you already Invoiced, for instance.

Resolution for Issue 'Can I apply an existing invoice to a sales order?' available: Yes (Solved).
Source: Intuit Community forum.

Can I apply an existing invoice to a sales order?: 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 invoiced
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Error Recovery for invoiced [Canada]
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