BTDF provides a library for modifying SSO Settings that it uses. The method is uses is slightly different from the default Microsoft sample SSO client, so take care regarding which one you're using.
Per that link, the class provides these methods:
namespace SSOSettingsFileManager
{
public static class SSOSettingsManager
{
public static void WriteSetting(string affiliateApplication, string propertyName, string propertyValue);
}
}
It should be fairly straightforward to call that method once you've added a reference to the SSOSettingsFileReader.dll in whatever C# project you have generating your password or updating it, i.e.
string newPassword = GenerateMyPassword();
SSOSettingsFileManager.SSOSettingsManager.WriteSetting("MyApplicationName", "Password", newPassword;);
You could also look at the source of how he's doing it if you want to implement the method yourself.