If both the free version and the full version were installed to the same folder, I'm afraid that uninstalling the free version will remove files that the full version needs to work correctly. This is because by default they both install to the same folder.
If you installed to separate folders, that should be fine. However, if you no longer have your ArtRage full installer and can no longer download it, send me an email to email@example.com with your purchase details and I'll arrange something for you so that you can easily reinstall the full version.
This is something we plan on changing for the next update - installing the free and full versions to separate locations. Sorry about the inconvenience!