This might be more information than you asked for, but it’s a useful primer for using CloudFlare 
Cloudflare serves as a middleman between your user and you, so when the user requests your site the request will first go to CloudFlare, and if CloudFlare doesn’t have the asset the user is looking for it will ask your you.
That means there are 2 separate connections - the one between the user and CloudFlare, and the one between CloudFlare and you.
You can disable SSL between you and CloudFlare, but that’s not suggested - the entire point of SSL is to prove that you’re you and nobody tampered with whatever you sent, so if you disable it, CloudFlare is arbitrarily trusting the data it receives and sends the data as you (since you gave it permission) which could be bad.
Now to answer your question, what happens to the LE certificate? Assuming everything is setup properly, it will continue to renew since the requests will be sent to your server. As long as you continue to use LE, the connection between you and cloudflare will be secure, just make sure to update your setting in cloudflare (Crypto -> SSL -> Full / Full (strict))