I appreciate the additional information you've given, @cpalmer. I've replicated in my end and the Billing Rate Levels is available in QuickBooks Enterprise. To isolate this case, we can fix this by performing the Rebuild utility tools in QuickBooks Desktop. 

This way, it'll return to its default order and automatically fixes minor company file data issues. Though, you need to back up your data first before performing these steps below to save your company data if file damage occur.   

Let me show you how:   

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.   

After rebuilding data, we can close and reopen your file to revamp it.    

However, if the issue still persists after doing the steps above, I recommend getting in touch with our Customer Care Team. This way, we'll be able to pull up your account in a secure session then run a series of tests to rectify the underlying issue.  

Before doing so, please check out our support hours to ensure that we address your concerns on time. 

Here's how to connect with our Customer teams: 

1. Sign in to your company account, then click Help.
2. Choose QuickBooks Desktop Help.
3. Hit Contact Us. 
4. Enter the question in the description field, then click Search. 
5. Select either Message Us or Call Us.      

Just a heads up, we have limited staffing and have reduced our support hours to 6 AM-6 PM PT Monday-Friday due to COVID-19. We will resume normal hours as soon as possible.    

Please let me know how it works. I want to make sure that everything is taken care of. I'm here to provide any additional assistance if needed. Have a good one!