When you use the upgrade option in the UI can it please start with the configuration as it exists now. If you go there and simply bump the image version which is the most common use then you lose ports, links etc.
The ports and links should be automatically copied over in your upgrade option. When I do an upgrade, I see my port and links.
What version of Rancher are you running?
You might also be hitting this issue with links. If they don’t show up in the UI, they won’t be copied over for an upgrade/clone.