One of the requirements during my product uninstall is to leave any files that have been modified by the user. Some files may be delivered by the installer others are generated by the program itself.
Also, I encountered a similar problem of it deleting folders on uninstall that originally had no data files in them when the software was installed but DID have data files at the time of uninstall. ( Our app created these data files as it was being used. These were folders those that would contain data generated by the user.)
What I did was to place a dummy file into the folder. I called my file "folder_placeholder.txt" and using the info from the above thread, marked the file to "permanent". That prevented the uninstall of the file AND its upper level folder structure.
Maybe you could create your dummy files and then your program can overwrite these files as it operates. On uninstall the settings should stick and leave the files that have the "user changed/created" data in them.
