Hi Fares,
Hmm… That’s odd… Generally our plugin only updates order status, and it’s not responsible for emails, so everything that is hooked to the order status change, including emails, should be processed as usual.
Are there any errors in “WooCommerce > Status > Logs” (you may also want to enable WP debug mode)?
As I understand this “Appointment Confirmation” email is a custom one, correct? How are you adding it to the completed orders? With some plugin, or custom PHP code?
P.S. If you wish, you can share admin account to your site, so I could log in and check what’s going on (my email is [email protected]).