Hi, I have noticed letsencrypt does not add alias domains to an existing certificate unless I turn SSL off then back on again for the particular website?
Yes, that's a known issue. The problem is that the SSL cert for a new domain can be requested only after the domain has been added to the vhost and is accessible on port 80.
So would it be better to have a checkbox on the page where you define the alias that says renew ssl, and if ticked: 1) After the vhost is created 2) The letsencrypt script is either renewed or ssl+letsencrypt is disabled then re-enabled automatically for this to work?
There is no checkbox needed and it would not help if it exists. it#s just something that we will have to work on for the next release to do a second pass of the config run automatically.