In the Organization page, check the file's component Permanent attribute.
However, as a general observation, it is a bad idea to install a file and then modify it to store user's data inside.
It is usually better to create a NEW file, using the installed one as a template. The new file will be in the user's documents or wherever and it will store all the new data. Of course, it won't be uninstalled.
How do I use the file as a template? If I install in the app folder, then copy it to "My Documents folder", that would work. Is this what you mean? If so, then can that copy be done by the installer on the first install, but not on updates? Is this possible with the Freeware version?
To use a file as a template you could use a custom action that copies the install file to another location. Then your application could use that copy to save it's data. To prevent the copying to happen on updates the custom action could check first if the destination file exists. If so, it should abort the copying.
This can only be done with the Professional version, since the Freeware version does not have Custom Action support.
A better solution would be that your application does that internally. It opens the template file, merges the read data with the user data and saves this to another file.