How do you keep user.config settings across different assembly versions in .net?

The next short solution works for me when we need to upgrade only once per version. It does not required additional settings like UpgradeRequired:

if (!ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.PerUserRoamingAndLocal).HasFile)
    Settings.Default.Upgrade();

I know it's been awhile... In a winforms app, just call My.Settings.Upgrade() before you load them. This will get the latest settings, whether the current version or a previous version.

ApplicationSettingsBase has a method called Upgrade which migrates all settings from the previous version.

In order to run the merge whenever you publish a new version of your application you can define a boolean flag in your settings file that defaults to true. Name it UpgradeRequired or something similar.

Then, at application start you check to see if the flag is set and if it is, call the Upgrade method, set the flag to false and save your configuration.

if (Settings.Default.UpgradeRequired)
{
    Settings.Default.Upgrade();
    Settings.Default.UpgradeRequired = false;
    Settings.Default.Save();
}

Read more about the Upgrade method at MSDN. The GetPreviousVersion might also be worth a look if you need to do some custom merging.