If not, can I download an update to the new edition as well as keep my markings/notes etc?
There is a new version of the Ellen G. White Writings Comprehensive Research Edition 2008, but it has been maintained to run on the current operating systems. There hasn't been released a new revision adapter for year 2017.
You'll have to access the official website to find additional information about compatibility and system requirements as well as changes implemented in the same version, but adapted to new operating systems.