It is normal for add-ins and scripts located in the installation path to be updated. I'm not sure of the exact process the update follows but it might be deleting the folder and then installing the latest version of the files. For example, for me the path that will get updated looks like this:
C:/Users/ekinsb/AppData/Local/Autodesk/webdeploy/production/7ca01d20fe2dafa65f944d9236f39fdec21b9b7a/
The sample files that are installed by Fusion into the above folder are read-only to help protect against someone making changes and losing those changes because of an update.
The default location for user-created add-ins on my machine is:
C:/Users/ekinsb/AppData/Roaming/Autodesk/Autodesk Fusion 360/API/AddIns
The files in this folder are NOT touched by an update or uninstall. You can also have add-ins and scripts at any location on your machine. It's just in this case Fusion won't automatically find them and you need to use the green "+" at the top of the "Scripts and Add-Ins" dialog to tell Fusion where they are and then Fusion will remember them after that. These files are also not touched by an update.