Guys, as Intel XDK is the only one officially supported C2 wrapper
We also officially support PhoneGap Build, so you can try that as well. You're not forced to use just the XDK.
xmnboy - if the problem is the .xdk file being overwritten, perhaps a simpler workaround is to export to a separate folder, then copy all the files over apart from the .xdk file? i.e. just update all the asset files and leave the same project file.
This problem is unfortunate but in this case it stems from a breaking change in iOS 10 and a lack of a reliable way to identify WKWebView - it's Apple who have put us in an awkward position over this :-\ We could add those old options back, but then apps are broken on iOS 10 again, so we would prefer to stick to WKWebView-only mode if possible - especially since it can be 2-3x faster!