Breaking the native AppStore update functionality would be something new... never heard about that.
Are you 1000% sure that this is what happening?
Do you have output of the native version and snapshot version in the app so you can confirm?
I know this sounds like me not believing you, but I had a similar problem once which cost me weeks and turned out to be a confusing mess of versions and bad feedback from C-level people 
The current "app store" version should be available as a snapshot anyway, just for consistency.
That is difficult to answer. The cordova 4/6 stuff shouldn't really be a problem, and can be tested locally with not much work. Fork the project, remove cordova and the platforms, readd the "old" version, see if it builds correctly.
What you should look out for are native changes: Additional plugins, other stuff in the native code that maybe changed and could cause the new snapshot to not work on the old native "container" any more.