Problem with SSL renewal

I had to renew an SSL certificate for the first time and I'm having some problems with it.

I ordered the renewal with the signing request that cPanel had stored, order went through with rapidssl fine. Then I pasted in the new key into cPanel, and it installed fine. However now when I log into my clients cPanel via WHM, its got 2 certificates, the old one and the renewal. If I log into their https site, its using the old certificate...

At this point I don't know what to do, so I tried deleting the expiring certificate from their cpanel but nothing happens, it says its been deleted but it still appears. I tried deleting it from WHM and I get the message...

Code:

File is still referenced in Apache: myclientswebsite.co.uk.crt

Does anyone know how I can resolve this problem? Can I still use this new certificate?

 

Resolved.... Backed up certificates and deleted everything (via SSH) to do with the sites certificates, deleted the SSL host in cpanel as well. Then I set it to a completely different IP and reinstalled the certificate. Bit of a pest because I had to reconfigure iptables for the new IP, but its working now so mod can close thread.