Hi there,
It's good you're catching up with your transactions. Doing this definitely saves you from the hassle of dealing with discrepancies in the future.
If you're not seeing a match due to the underpayment, I recommend going through your bank feed, locating the transaction in question and clicking on Find Match. This allows you to match your transactions when they're not automatically showing up as a match option. Check out this helpful article for more info: Match and categorize bank transactions in QuickBooks Online.
When invoices you send in QuickBooks become uncollectible, you need to record them as a bad debt and write them off. This ensures your accounts receivable and net income stay up-to-date. There's a helpful article which shows you how to do this. Check it out using this link: Write off bad debt in QuickBooks Online.
In case you have other questions, feel free to contact our support team using this link here.