I originally created one certificate will all the domains in the single certificate. but eventually some of the sites in that certificate were deleted/moved to a different server. So that caused problems when renewing the certificate as some of the domains failed for the DNS challange, and I could not renew any certificates.
So I started creating certificates separately for each site and that has hit rate limit and I can no longer issue new certificates (until next few days)
So what is the best strategy for issuing and renewing certificates without hitting the rate limit and also not being affected if I delete any sites.
Do you mean you change the subdomain name ? as changing the latter part of the URL will make no difference to the certificate.
With only about 20 domains, personally I'd add them as single ones. If you create them at a rate of 3 per week (you don't need to remove them from your single cert), and auto-renew when they have 30 days left ... you will manage to have certs for all your subdomains, and the ability for the occasional mistake or new cert before hitting the current rate limit of 5 per week.
If all the sites are in a single cert, then the cert has an expiry date ( not per domain) so that would need to be renewed just the once ( for all domains ) if you were doing it that way.
It is if you have added them all to a single certificate. You don't have to though, and you can have separate certificates - one per subdomain ( or subdomain and www.subdomain if you like )
correct
if you have the renewal cron only renewing certificates that are due for renewal ( that depends on exactly what command you put in the cron). Then you can run it weekly, or daily ( as I do ) and it will automatically renew any certificates that are within the specified days of renewal ( usually 30 days by default).