Some time ago, Microsoft replaced the application Skype UWP with a newer electron version in the Store. Due to this update, the Skype has lost some of its features, which Microsoft is now restoring to the latest version of the application.
The transition from UWP to an Electron app was not smooth, but allows developers to easily customize the Skype on many more platforms, such as Chrome OS.
A new version of the application 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