Token Frenchboy

Hi, I wanted to re-issue a certificate issued a while back because I needed to reinstall and had lost the private key. However, I think I've made a mistake. I first thought by revoking it, I could then renew it but of course the certificate is still there. In an effort to tidy up, I found the certificate in the end entity and deleted it there, but this has probably made it worse: I cannot generate the certificate as it says the old one is still there, but how do I tidy it up or configure the system...