I apologize for answering my question by myself, since I found the solution right after posting it. This question gave the answer basically: Save and reload app.config(applicationSettings) at runtime
I had to use this code, to write to that section 'applicationSettings':
// this gets the applicationSettings section (and the inner section 'inoBIBooks.My.MySettings')
Configuration config = WebConfigurationManager.OpenWebConfiguration("/" + targetvdir);
ConfigurationSectionGroup applicationSectionGroup = config.GetSectionGroup("applicationSettings");
ConfigurationSection applicationConfigSection = applicationSectionGroup.Sections["inoBIBooks.My.MySettings"];
ClientSettingsSection clientSection = (ClientSettingsSection)applicationConfigSection;
// set a value to that specific property
SettingElement applicationSetting = clientSection.Settings.Get("BIDB_Username");
applicationSetting.Value.ValueXml.InnerText = "username";
// without this, saving won't work
applicationConfigSection.SectionInformation.ForceSave = true;
// save
config.Save();