A part of the .NET Framework that provides a unified programming model for building line-of-business desktop applications on Windows.
It is necessary for you to set the correct ,net framework version if you want to renew the certificate.
It also depends on if you use automatic update or program update and whether it is a test certificate or a certificate provider. For more details, you could refer to Certificate Expiration in ClickOnce Deployment and ClickOnce and Authenticode.
If your customers have to uninstall and reinstall manually, they will lose any data that you might be storing in the ClickOnce DataDirectory. In the uninstall/reinstall application, you can move the data, and in the new version, you can find the data in a new location. You could see the details here.