QB Issue Resolution:

When you do a search, use the advanced setting.  Filter it to invoice number.  If you click save and new, you should not get duplicate invoice numbers.  You can also look in the list of sales.

You may also want to look at how you are doing the billing to see if there is a procedure that will eliminate the duplicate billing.

I have also found that the search feature is not reliable in some cases.

Resolution for Issue 'Searches are not getting results, they did in the past. A recent search using custom field one did not get a result, if entered info by invoice for the same I do.' available: Yes (Solved).
Source: Intuit Community forum.

Searches are not getting results, they did in the past. A recent search using custom field one did not get a result, if entered info by invoice for the same I do.: 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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