Has Jeppesen announced plans to stop supporting the Microsoft platform for Flight Deck Pro?
Only 6 months ago Jeppesen announced a common interface for iOS 9 and Windows 10.
And why would they deliberately lose their airline customers that use Windows? The integrated Class 3 EFB's on Boeing planes for example, run Windows.

The open architecture of the EFB
Class 3 system will allow airlines
(or third-party suppliers) to develop
software for the Microsoft Windows
processor using a software development kit provided by Boeing and
Jeppesen.

Regarding the FliteDeck, only a couple of weeks ago:

ForeFlight and Jeppesen Announce Strategic Alliance
Jeppesen and ForeFlight will work together on a next-generation release of FliteDeck Pro for both iOS and Windows that will deliver a combination of the familiar capabilities in FliteDeck Pro and significant features and functionality from ForeFlight Mobile.