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If you create and run a package to uninstall the app first, you can create and run a package to install the app with different settings. See how to do both above!
It's common for an email generated by an app to be flagged as spam by default. Check your recipient email's spam folder and mark the email(s) as "not spam" and they should arrive correctly after that
While you technically can by assigning the MSI to an OU, it won't include the email settings if you do it that way. So you will need to script the copying of the email_settings.xml file to the application folder on the devices afterwards. See the video on using PDQ Deploy above for more info