When using the built-in .Net application settings infrastructure, the user settings are lost when the primary assembly version number is upgraded if you dont explicitly upgrade the settings.  Thankfully, the .Net framework has taken care of the details.

Basically, this is what you need to do:

1.       Add a Setting to your application called UpgradeSettings and set it’s default value to true.

2.       On startup, or when you check for updates, look at this setting.  If it is true (it will be false if you have lost your settings due to an update), then call the Upgrade() method.

3.       Set the UpgradeSettings setting to false.  This will prevent startups from calling Upgrade until the next time it is needed.

4.       Save your settings.

Example:

Sub UpgradeMySetings() 

        If My.Settings.UpgradeSettings Then 

                My.Settings.Upgrade() 

                My.Settings.UpgradeSettings = False 

                My.Settings.Save() 

        End If 

End Sub 

And here is Microsoft Documentation on the relevant method.

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