This is explained by CloudFlare here: https://support.cloudflare.com/hc/en-us/articles/214820528-How-to-Validate-a-Let-s-Encrypt-Certificate-on-a-Site-Already-Active-on-Cloudflare
In particular, they say:
"the default method used for ACME authentication by the Let's Encrypt client utilizes the DVSNI method. This will fail for a domain which has Cloudflare enabled as we terminate SSL (TLS) at our edge and the ACME server will never see the certificate the client presents at the origin. Using alternate ACME validation methods, such as DNS or HTTP will complete successfully when Cloudflare is enabled."
Then they provide instructions to use the webroot method for SSL creation.
If I use this method, will it conflict with the built-in Vesta method (the GUI and checkbox), and if so does anyone have any recommendations on the best way to proceed?
Thanks in advance.