The update of device-based VPP applications is only officially supported on iOS 10.3+.  So, if you have some devices that are on a lower version of iOS, you can either:

• Update all devices to iOS 10.3+ so that you can benefit from the ability to update their Device-based VPP applications.
• Accept that your devices running a version of iOS lower than 10.3 will have to uninstall and reinstall their Device-based VPP applications.
• Convert your VPP licenses to user-based.  This is discouraged and only to be used as a last resort.

 For more information on the procedure to update regular or VPP App Store applications, please see the this thread.