Let me flesh out the answer a little: When you install a file with MSI it points to it with a component GUID. The MSI file thinks it "owns" the file since you have given it a unique GUID and will happily delete the file on uninstall (this can also happen as part of a major upgrade), even if you have modified the file and it is full of user data. This is a very common design-flaw in many setups.
You can work around this by setting the component permanent as described in this answer: MSI Reference Counting: Two products install the same MSIs. However a better concept is to install only read-only files and use your application itself to initialize user-data (ini files, databases, xml settings files, etc...) by copying the read-only templates to the user profile and / or set them via application internal defaults (defined inside the source code). This decouples the deployment of user-settings and data files from the installer avoiding accidental deletion of user data and allowing you to treat all user data setup from the application with the increased flexibility and control this yields. And you avoid complicating your setup, which is more than complex enough as is described here: What is the benefit and real purpose of program installation?
Many people feel that their setup should uninstall all user data. Don't go there. My take on this, and many with me, is that anything modified by the user is user data and should be left alone in case the user reinstalls the product or if they want to keep their data for import into other applications. You can instead document where data is stored and let people or system administrators clean this out manually. Cleaning out all user data would involve cleaning all user profiles. Though you can use concepts such as ActiveSetup to accomplish this (another ActiveSetup explanation), it is generally more trouble than it is worth and error prone.
For more understanding of the component GUID concept see this answer: Change my component GUID in wix? (recommended read for your use case). Here is a discussion on installsite.net on how to initialize and update userprofile and user data: http://forum.installsite.net/index.php?showtopic=21552
Similar answers (for tracking) - I keep writing the same over and over ;-):