After downloading the .zip file you have to manually update your theme below are the instruction to update the theme:
First activate the different theme and delete the Clean Retina Pro theme from your WordPress Theme directory. (Note: make sure that you have not customize the code. If you have customized the code then your customize code will be lost. So, Please back-up you old version before deleting it)
After deleting the old version now upload a new version of Clean Retina Pro theme and activate it.