how to renew our SSL certificate?

as the subject says.
we have 3 certificates from GoDaddy, one bundled, one intermediate, and the other one is the SSL cert.
certificate is of SHA-2 type.

How to renew the existing one?
I followed this link on step #3 but complaining that I already have the alias.
so I run this command: keytool -delete -alias root -keystore sdp.keystore
~I've ran the command for each of the alias created

after that, I re-add the alias pointing to the new certificate files (pointing to the bundled cert, then the actual SSL cert).
After following the rest of the steps, (copying the keystore file and restart the services), site doesn't come up.

Please advise.
Thank you in advance.

UPDATE:

tried to re-key the certificate with SHA-1, no luck
http works, but not https
only installed the bundled cert and SSL cert, ignoring the intermediate
no complain but still doesn't work