I'm here to help get this auto-populate working for you.
Generally, the invoice created out of an estimate should auto-populate the email address once you choose the customer. As long as the customer's information has the email address, it should just work fine.
Let's try using a private browser first to check if this could just be a browser issue. Here are the keys you need to press to switch to private browsing:
Google Chrome: press Ctrl + Shift + N
Mozilla Firefox: press Ctrl + Shift + P
Internet Explorer: press Ctrl + Shift + P
Safari: press Command + Shift + N
If the private browser does not show the same behavior, you can continue doing your tasks in your QuickBooks Online account on a regular browser. You can switch back to the regular browser (Ctrl + N) then clear your browser's cache.
However, if the issue persists, it'd be best to reach out to our Online Specialist to check this further. They have extra tools to access your account securely and help perform other steps to get this resolved.
That should help get you in the right direction. Keep me posted if you have other questions about the auto-populate fields in your transactions. I'm here to help. Have a great weekend.