Recently I went through this to update a Cert on a Gatewat: http://fixmyitsystem.com/2012/07/configure-citrix-xenapp-web-site-to-use.html

However the SSL certificate was still not updated

If you route traffic over a different port you need to run through this as well : 

Start , All Programs , Citrix , Administraion Tools , Secure Gateway Configuration Wizard

Choose Next and Standard

Pick your new Cert

Leave the rest of the options as default