thealienguy: I also had to uninstall and reinstall to get it to work. However when I uninstalled it I was asked if I wanted to keep my saves. I clicked yes and then installed it fine and still had my saves. I use windows myself, so I don't know if the windows uninstaller is different from the mac version.
The Mac version of Galaxy absolutely did NOT ask me if I wanted to save my save files. However, most GOG games on Mac, manual installs or Galaxy installs, come as a single app package, not as a folder, and they store their save data in a different directory to keep them safe. For some reason, Starbound comes as a folder with the save data kept inside, so deleting the game takes the save data with it.