So, you have a brand new Windows Phone Silverlight 8.1 application and you wish to publish an updated version with a lot of new features or not that many. And all these for a enterprise app distribution…
In WP8 you used to built a new XAP file and sent it for deployment, but in WP Silverlight 8.1 that will not succeed. Digging deeper to MSDN you will find a small closing paragraph on an article about application publishing for WP Silverlight 8.1, stating that you will need to manually increment the version number of the application, which can be found under the Version attribute of the Identity element in the Package.appmanifest file. This version number is not automatically incremented for Silverlight 8.1 apps, but it is essential being greater than the previous version for the package to be recognized as an update.
Further reading: Prepare your Windows Phone Silverlight 8.1 app for publishing
Happy updating your XAP files!