YU has confirmed that they are still in partnership with Cyanogen and in fact will be rolling out the next Cyanogen update by end of this month. The next Cyanogen version is currently being beta tested. YU had recently launched their existing smartphone running Pure Android, instead of Cyanogen.
YU Yuphoria and YU Yureka are now available running pure Android version. YU has given this option (their handsets running optional Pure Android or Cyanogen) based on the user feedback they had received. Many users had requested for pure android experience, others were happy with Cyanogen.
YU and Cyanogen partnership is still intact and they will continue providing customized experience to their users. Those using YU smartphones running Cyanogen watch out for new updates that will be rolled out by end of October. That will be Cyanogen OS 12.1. You can check the details here.
YU will be launching the Yutopia soon, a high end smartphone that probably will also be running optional Cyanogen OS or pure Android.