Ouch, that’s unfortunate 
If you still have the private keys, you should be able to get the certificates from crt.sh
If you have the certs, you can recreate the fullchain by downloading the intermediate from here and concatenating it to the end of the cert.
If you don’t have the key, it sounds like the rate limit you ran into was probably the duplicate certificates limit, so you might be able to issue a new cert with a slightly different set of domains (eg separating www and non-www into different certificates or combining them into one).