IIRC Ubuntu disables all third party repos as part of the upgrade process. Typically it leaves 3rd party software installed but in this case there is probably some package that salt for ubuntu 16.04 depends on that isn't present in 18.04 and as a result the package manager is actually removing your salt install. It
should leave your configurations in place so after the upgrade you should be able to re-add the salt repository, reinstall salt for Ubuntu 18.04 and pick up where you left off. That being said, you might end up upgrading salt versions as well which could complicate things. Do you know what version of salt you are running on 16.04? Is that same salt version available for 18.04?