One of the most user friendly additions to software, ever, is the undo button. (if you want to feel how it is to use software without, try Linux in terminal for a while ;) ). And one of the best attempts to do this on a OS scale, is Time Machine. It should be as easy as bringing up a prompt and step or scroll backwards in time. You are really just stepping between data states. If you restore a state, it will merge with current state and step forward (which of course can be undone). You can decide to restore only one app, and thereby limit impact.

Update, restore, "are you sure you want to do this?", "pick the right destination", etc are user unfriendly concepts, and will make people nervous. Auto-update apps, but let people undo. Make restores undoable. Change "are you really sure?" to "don't worry, you can always undo".

Of course, you could argue, this will waste storage space. Well, with a good diff algorithm to rely on, not really that much. And even if so, you can always merge older states together (e.g. the detail of change is mostly relevant to very recent events - a few weeks back, I only care about major things like when I deleted all my contacts and didn't realize until now).