Since the domain/site has an ssl, the vhosts file for the ssl is separate and also needs to be updated. Not just the normal port 80 entry.
vhost (:80)
my-wp-site.com.conf
<VirtualHost *:80>
...
DocumentRoot /home/ubuntu/sites/my-wp-site.com
...
<Directory /home/ubuntu/sites/my-wp-site.com>
Options Indexes FollowSymLinks
AllowOverride All
Require all granted
</Directory>
...
</VirtualHost>
vhost (:443)
my-wp-site.com-le-ssl.conf
<IfModule mod_ssl.c>
<VirtualHost *:443>
...
ServerName my-wp-site.com
ServerAlias my-wp-site.com
DocumentRoot /home/ubuntu/sites/my-wp-site.com
<Directory /home/ubuntu/sites/my-wp-site.com>
Options None FollowSymLinks
AllowOverride All
Require all granted
</Directory>
...
</VirtualHost>
</IfModule>
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