I appreciate you for getting back to us, Ian.

Allow me to grab this opportunity to help you fix the issue you're having with your invoice.

I recommend toggling your progress invoicing to ON and OFF to isolate this issue. Let me show you how in your QuickBooks Online (QBO) account.

1. Go to the Gear icon and select Account and settings.
2. Select the Sales tab.
3. Click  the Progress Invoicing section.
4. Toggle the Create multiple partial invoices from a single estimate radio button to OFF.
5. Click Save and then Done.
6. Repeat steps 1 to 4 and toggle the radio button to ON.
7. Click Save and then Done.

You can also check this article for more details: Set up and send progress invoices in QuickBooks Online.

If the issue remains, I recommend logging in to your account on a private or incognito window to verify if this a browser cache issue. Cache files that are stored for a long period can cause unusual behavior that affects the performance of your account.

Using a private window is a great way in identifying this kind of issue as this doesn't save any cache files. To open an incognito window, you can refer to these keyboard shortcuts:

• Press keys: Ctrl + Shift + N (Google Chrome browser)
• Press keys: Ctrl + Shift + P (Mozilla Firefox & Microsoft Edge browser)
• Press keys: Command + Shift + N (Safari browser)

If you’re able to create your second progress invoice with ease, I’d suggest clearing your regular browser's cache. This will delete all saved data files from your browser and start with a clean slate. If the issue remains, I recommend using other supported browsers. This way, we can check if this is a browser-integrated issue. 

Once your customer pays their invoice, you can refer to this article on how to record it in your account: Record invoice payments in QuickBooks Online.

Keep me posted if you need further help in managing your invoices. I'm always around ready to help you. Stay safe!