Hi. Sorry I missed your response.

The site does not break if I garble up the .htaccess file.

Indexes are enabled because I saw that in another post when someone had the same issue and that resolved it for them. Honestly, no clue what that does; just tried it. :)

AllowOverride All and Require all granted in the parent directory is another unknown to me. Following examples from those previous to me with similar issues.

No, there is no .htaccess file in the parent directory of /home/ubuntu/sites.

Missed your reply too. (I think we need to @fischgeek the user in chat to send a notification.) I see you've resolved the issue now - so all good. (Must admit I also overlooked the separate HTTPS vHost container as well.)

> Indexes are enabled because...

Options Indexes is unrelated to this issue. Indexes enables Apache generated directory listings when a directory index is not present in a directory. So, this should generally be disabled for security reasons, otherwise, it potentially exposes all the files you might have sitting in a directory - it can also be indexed by search engines (without additional steps), which would be undesirable.