This is sort of an aside regarding your comment on WAB. It's really not much work to switch from WAB to WABDE and it gives you additional options to mess around with the code and test changes without having to work in your production environment.
The 10.9 upgrade ate every one of our WAB projects (they all broke and Esri was unable to do anything to help) so to recover we immediately migrated 100% to using WABDE (aka WAB Developer Edition) and we've been there since May.
This provides more "distance" between ArcGIS Enterprise and the applications, they now live outside it in a separate folder in the web server where future upgrades will be totally unable to touch them. (All of MY apps were already built with WABDE and were completely unscathed by the 10.9 upgrade!)