Hi rajanrawal
There are actually 3 keys in play for an issuance of a SSL Certificate
A) Your account key. This is what you use to authenticate against Lets Encrypt
B) A CSR key. You don’t see this or need this as ZeroSSL takes care of that
C) A Private Key for the domain
D This can be easy to miss sometimes so when the certificate is issued you should have downloaded two files
Options:
A) If you still have the CSR and your Account Key (A) paste both into ZeroSSL and I am not sure on the internals but I believe lets encrypt will let you re-download the Domain Key (there may be a timeout period)
B) Revoke the certificate and then reissue it again for the domain. You can’t revoke using ZeroSSL but you will be able to reissue the certificate that way. You will need your account key to revoke the certificate and create a new request.
Andrei