Yes, all of your settings will get overwritten by the pre-built website content. Also, I do not think it's that necessary, because it will change only the type of header, colors of the website and some behaviors on images/shortcodes.
We suggest to do it manually - at least you will know what did you change. Also, to change the colors, you can use the "Theme Skins" (Theme Options > Colors > General), change the "Custom Skin" to some color. If you would have to reverse that, just change it to "Custom Skin" http://prntscr.com/n9fqaz
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Also, I do not think it's that necessary, because it will change only the type of header, colors of the website and some behaviors on images/shortcodes.
We suggest to do it manually - at least you will know what did you change.
Also, to change the colors, you can use the "Theme Skins" (Theme Options > Colors > General), change the "Custom Skin" to some color.
If you would have to reverse that, just change it to "Custom Skin"
http://prntscr.com/n9fqaz
Thanks