Yes you would lose your savegames from uninstalling, although you can just unlock them again from the Options menu.
If you really don't want to lose your savegames and don't like the idea of simply unlocking them again, it's also possible to back them up along with your user preferences. There's a file in the Eufloria\Resources\ folder called "user.settings". Make a backup of this file before you uninstall the game. Then, after you reinstall, copy the backed up user.settings to its original location in the Resources folder before you run Eufloria.