my environment variables are not updating

I am self hosting appwrite. I update the .env file located in the appwrite directory on my instance.

I run
docker compose up - d

After it finishes, I run:

docker compose exec appwrite vars

However, the values I updated in the .env file do not show up here. Values I am trying to update:
_APP_EMAIL_CERTIFICATES
_APP_SYSTEM_SECURITY_EMAIL_ADDRESS

My _APP_DOMAIN AND TARGET is of the format app.example.com

(I was updating above variables so that my certificate generates properly for my app.example.com , which currently shows an insecure connection)

Looking for any help. Thank you.

Little update....the secure connection is getting established now, had to clear browser cache and cookies.

However, the variables are still not showing as updated in the appwrite vars command