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The problem is that, on the Cpanel, there are folders that automatically create after few hours even after deleting.
As a result, those folders contain .well-known folders.
The Wordpress website has a translation plugin called wpml. Normally, these translations do not have folders but the folders for each language keeps recreating itself with only .well-known folder in it.
This development stops other translations from displaying in the website
Thanks for that. It doesn't sound like a Let's Encrypt problem
HTTPS connections to your site (via Cloudflare proxy) are working fine. The HTTPS connection is what certificates are for and those are working fine.
The application configuration (WordPress in your case) is beyond our scope. You should ask the cPanel support about that. Or, possibly the Wordpress wpml support people. I am sure a quick google will find those forums.