I feel your pain. An update to a new version of BootStrap was just applied to our application under test... and of the 121 test cases we have defined for it, all of them failed. The reason for our failures are all object identification issues. Either the new version of bootstrap has altered the hierarchy of the objects (added or removed a DIV panel) or some other identifying factor has changed (objects that used to have an object label no longer do, className property has changed in value, etc).
For us, there's not a lot that the development team could do. However, one thing that has remained consistent is that, when we're using the ObjectIdentifier or idStr property, that stuff hasn't changed. While hierarchy changes are a bugger to deal with, there is some mitigation that can happen where you implement the "Extended Find" to account for some of those differences.
However, ObjectIdentifier is your key. I don't know if you're testing a web app or a desktop app, but either way, if you can have your developers give you at LEAST one property on every object that has a static identifier, that will make your object identification issues MUCH less painful. It won't take them ALL away, but it will at least give you a consistent scheme where your application will always identify the same objects with the same properties.
