I've some info on why your Profit & Loss report isn't showing some of your paid invoices.
One of the possible reasons it happens is that the report you're using is already memorized. Once you use a categorized report, it will only show the data that is included in the filters.
If this is the case, you can go back to the P&L report and revert its display. Just click Customize Report and select Revert to undo the categorizations.
It's also possible that the dates aren't properly filtered. Let's make sure that it is matched to when you exactly recorded the invoice payments. This will also help us identifying if the issue is within your company file.
If you've already done the following steps, I'd recommend updating QuickBooks Desktop to its latest release. Doing this action will help resolve some minor issues within the program.
If you're still getting the same result, run the Verify and Rebuild tools. The Verify Data self-identifies the most commonly known data issues within a company file while Rebuild Data self-resolves most data integrity issues that the Verify Data finds.
Additionally, you can check out this article for more details on customizing your reports in QuickBooks Desktop. This would help you in viewing the details that matter the most to your business.
Just tag my name in the comment section if you have any other concerns or questions. I'll get back to you as soon as I can. Stay safe.