Some time ago, Microsoft replaced the Skype UWP application with a newer electron version in the Store. Because of this update, Skype has lost some of its features, which Microsoft is now restoring to the latest version of the app.
The transition from UWP to an Electron app has not been smooth, but it allows developers to easily adapt Skype to many more platforms, such as Chrome OS.
A new version of Skype from the company Store now lets you reply to chat messages directly from notifications on the Windows 10 desktop.
You can try the new application from here