Updating to 3.9? It won’t affect the theme or how it looks.
You can update by deleting the old version and uploading the new version. Only do this if you haven’t made any changes to your theme/appearance. If you have made changes to your css or any other files, you can compare the differences in code using diffchecker.com If you’ve made a lot of changes, then don’t worry about updating Epik, it’s not a requirement, the only differences are slight enhancements to the appearance, but nothing major.