That error means somebody (either on that server or on another server on your domains) got a duplicate certificate containing the same set of domains successfully. If you had run into the TLS-SNI issue, you would’ve received an error similar to the one described in Solution: Client with the currently selected authenticator does not support any combination of challenges that will satisfy the CA). Based on that, it looks like your cert renewed properly?
If not, there’s no way to reset the rate limits manually, so you’ll have to wait for the rate limits to expire as described in https://letsencrypt.org/docs/rate-limits/). If you post your domain here, we can look up your domain and see which certs have been issued (Let’s Encrypt logs this info by default, so hiding your domain here doesn’t do much). If you’re hesitant, you can check yourself at https://crt.sh to see how many certificates have been issued for your domain.