Hello @DevelopDaily,
You get the error because revoking a cert has no effect on rate limits. Anyway, a few days ago Let's Encrypt implemented an update into the boulder (server part of Let's Encrypt) that will allow to renew a cert without increasing the rate limit for your domain (the renew should be for exactly the same cert, if you want to add or remove a domain in the cert it will increase the issued certs for your domain). As I said, this feature is already implemented in boulder but they need to fill the database with all the previously issued certs so, it could take a few days but they will announce this new feature here.
Cheers,
sahsanu