If you have downloaded the .zip version of Sims 4 Studio instead of the Installer version then you need to extract the contents of the .zip to a folder, open the folder, and click the S4Studio.exe in order to run it. The Installer version will install Studio for you and then you can click the Studio icon to run it. Many people feel more familiar and comfortable with the Installer version and you can download that
HERE.
Sims 4 Studio will not damage your files when merging them. Before Studio added the ability to merge .packages many people were using s4pe for merging .packages and s4pe
has been reported to damage some files when it is used to merge .packages. This is probably what you're referring to. For some .packages, if s4pe is used to merge them, it will damage them to the point that when the merged.package is placed in the Sims 4/Mods folder the game will not start so I do not recommend using that tool for merging .packages.
There is a tutorial showing how to use Sims 4 Studio to merge .packages
HERE.
Currently Studio is working on adding new functionality to its
custom content management feature that will allow you to unmerge merged content and we're expecting that to be out in the next version :)
