If you have modified the parent X theme directly, regretfully, it will remove all customizations you have done. In that case, it must be repaired by a third-party developer as we do not provide support for theme modifications.
In WordPress, it is widely known that if you're going to customize a theme, you must do all customization in a child theme. You can read more about this in our theme customization guide at https://theme.co/apex/forum/t/customizations-best-practices/205
Regarding the validation issue, it's possible that this is a result of version incompatiblity between X and Cornerstone. You're using X 6.0.4 and Cornerstone 3.1.3. As you will see in our Changelog, X and Cornerstone versions are released in pairs. If one version is off, that could cause compatibility issues. Please try uninstalling Cornerstone and go to WP Admin > X > Validation so that X will automatically install the compatible version of Cornerstone.
Hope that helps.