I don't know how you did it and what unpacking program you used but:
The mod is available on Moddb since many months and a similar installation Instruction is used on GitHub as well to get the Early Access of the Current Development Stage for the next Version. If that were the case, I would have already been informed by the people on Moddb or on my own Discord Server and changed the installation instructions accordingly.
The Overwrite of the Gamedata and Mod Folder doesn't delete any other Files or Folders, which are located in these two Folders. It just adds the Commander Survival Kit Folder or the .scd File to these two specific Folders. I use this Install Instruction personally several times and my other Folders and files are still available after doing this. Even other Mods are using a similar Install Instruction sometimes and didn't get any File Loses after that so far. This is mostly the Faster Way to Install a Mod instead of manually Copy and Paste them into these Folders.
Update:
I just tested it again myself to be Sure and it works exactly as I described in the Current installation instruction or above. All other files and folders still exist in these two Folders and have not been deleted by the Overwriting Process. However, I agree that there is a risk when using this method. So I will expand the installation instruction using the method Rama described above in his Post as an alternative Installation Instruction. If there are people who don't want to overwrite the two folders, they can follow the alternative Installation Instruction, which is mentioned above.