Hi there, @JenFleet. 

Thank you for reaching out to the Community. Let me share you some insight about class tracking in QuickBooks Desktop. In QuickBooks, you can create classes that you assign to transactions. This lets you track account balances by department, business office or location, separate properties you own, or any other meaningful breakdown of your business. 

If you wish to run report that show the invoice, payments and for the specific company, you can pull up the Customer Balance Detail Report. I'll show you how:  

1. Click Reports at the top menu bar. 
2. On the drop-down list, click Customers & Receivables and choose Customer Balance Detail. 
3. Hit Customize Report.
4. From Filters, search Class.  
5. Drop-down arrow from Class and choose the specific company you want to show in the report. 
6. Press OK.

Once done, the changes will take effect. And you can email it to your buyer either through Excel or PDF.  

However, if the payment still disappear once you filter the class, we can perform basic troubleshooting steps to fix the issue.  

There are some reasons why this occurs, which may cause damage data, and we can fix this by performing the Verify data and Rebuild utility tools in QuickBooks Desktop. This way, it'll return to its default order and automatically fixes minor company record data issues. Though, you need to back up your data first before performing these steps below to save your company data if file corruption happens.   

Let me show you how:    

Verify Data: 

1. Press the File menu. 
2. Choose Utilities from the drop-down option.  
3. Select Verify Data. 
4. Tap Ok to continue.   

Rebuild Data:

1. Click the File tab at the top. 
2. Select Utilities from the drop-down option. 
3. Choose Rebuild Data. 
4. Click Ok on Rebuild has completed.    

When the verify/rebuilding data finished, we can close and reopen your file to revamp it. Or restart your computer to refresh your QuickBooks data.   

Here's a couple resources related to Reports that you may find useful: 

• Set up and use class tracking in QuickBooks Desktop 

• Filter, sort or total reports by Class 

That's it. Please let me know how it goes by clicking the Reply button. I'll be here to extend my hands with you. Take care!