Firstly, you have to define what is it you mean by a pop-up? In web world a pop-up is a new window that is opened by a webpage without an explicit command for the user. It is usually a hindrance to the user experience and most of the people use a popup-blocker to avoid such things.
So, it might not be a good idea to give important information about the site update using a pop-up.
If you just want to send the update information, one simple way how people do this is by taking the email-id of the user and send the update information via a mail.