Thank you so much, that helped me figure it out. I was able to renew the certificate using portecle and following the instructions on the documentation. Although the documentation is for windows, it was still very helpful for the VA appliance. All I did was:
1. Copy the existing keystore_new.jks file from the virtual appliance on this path /usr/local/webhelpdesk/conf to my windows desktop.
2. Open the key store using portecle
3.Delete the existing keypar with the old CA reply.
4. Generate a new key pair (give it the alias "tomcat" or it will not work) and csr just like it says on the documentation you provided.
5. Submit your csr to your certificate issuer
7. Download your CA reply in a .pb7 bundle with the root and intermediate certificates included in one .pb7 file
8. Right click on the key pair created on step four.
9. Import your CA reply and save they keystore.
10. copy the new keystore back to your virtual appliance replacing the existing keystore on /usr/local/webhelpdesk/conf
11. restart the whd service.
and that's it! it worked perfectly fine.