Allow me to provide some insights and instructions on how to get past this issue so invoices will now show as paid.
When receiving payments in QuickBooks Online, you'll need to make sure that the payment is linked to the correct invoice so it will show as paid.
Once verified and the problem continues, I suggest accessing your QBO using a private window. This lets you utilize your data on a clean slate and helps determine if the issue has something to do with your browser.
If it works fine, you can go back to the regular browser and clear its cache.This eliminates the unnecessary file to prevent this hurdle from happening. Web-based platforms like QuickBooks Online collect cache files for faster browsing. However, too much may lead to unusual behavior.
Lastly, you can always scan through these links below about processing invoice payments in QuickBooks Online and generating reminders for overdue invoices. Just in case you need them for your future transactions: