Steve
We moved to El Capitan a few weeks ago. We ended up in a cycle of upgrading quite a few things at the same time.
I can't remember all the details as away from main machine but we ended having to upgrade Xcode to 7.0 from 6.x, we ended up upgrading Cordova which meant whitelists, we also ended up upgrading a fair few plugins as well which also introduced other changes as the plugins had updates.
I recall that compiling for iOS 9 required Xcode 7 so that may have been the catalyst.
I know we put a lot of work in to get back to the same place we started from.
My suggestion would be to hold off the Xcode and OS upgrade until you have upgraded plugins and got the rest of your software stack in good order. When you have the latest plugins, latest stable Cordova etc then upgrade as you want. This is the opposite to us as one thing after another forced us to upgrade quicker than we wanted.
The other think I would also suggest is getting a Carbon Copy Cloner backup sorted out before the OS upgrade. It works very well and gives you the easy option of going back just in case.
Rob