The command you’re looking for is
ee site update domain.com --ssl=le you can also add the --wildcard flag to that if you need a wildcard cert.
See this page for more info https://easyengine.io/commands/site/update
EE will automatically renew your certificates for you, but if you’re using wildcard certs there are extra steps you need to take (using Cloudflare DNS). See this page for more info on how to renew your normal certs and wildcard certs manually if you ever need to renew it yourself or if you’d like to renew certificates for all your sites in one go: https://easyengine.io/blog/easyengine-v4-0-10-released#ssl-renewal
I recommend reading through the Commands page to familiarise yourself with the new command structure in ee4, it’s very easy to get the hang of it