The previous response that you received on this topic was correct, though: if you do that, you are doing it wrong -- your program has a bug. You should fix that bug instead of ploughing ahead anyway. While it may appear to work for some users, that just means that your testing is incomplete and you and your users will run into trouble eventually.
In a PrivilegesRequired=admin installation (the standard and recommended approach), the installer itself should only install per-machine things (e.g. HKLM or {pf}). Meanwhile your application does not run with admin privileges and while it can read per-machine settings it cannot write them. So while you can save some defaults at install time, the actual active settings must be stored per-user (e.g. HKCU or AppData). This is especially true because the installer is run only once, but the app might be run by either multiple users or just a different user than who installed it (think of a business machine where an IT admin installs it, but that's not the day-to-day user of the app). It might not even be possible for the installer to access the per-user settings of the day-to-day user (nor should you try).
The installer can install and upgrade those per-machine defaults, but any installation or upgrade of the actual per-user settings must be left to the application itself, and may need to happen more than once (as different users run the new version for the first time).
For upgrading those default per-machine settings, it's usually sufficient to use flags to avoid overwriting existing files/values, but you can do something more complex if you wish. Usually the trigger to detect that is simply that they already exist, possibly with some app-specific check to determine that they're outdated in some way.
You can relax some of this by making a per-user installation instead of a per-machine one, but this is not recommended for most apps -- it limits what things can be installed (and where), wastes disk space if the app is needed by multiple users, and bypasses some security rules that IT admins like having around.