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I was using my computer normally when I got a "Updates Available" notification.

On selecting to update, the App Store opened, and I saw 3 updates available: 1) iTunes 2) Java (I have never installed Java myself, as such.) 3) Evernote

I selected the option to Update All. A few seconds after the update process started, I got prompted to enter the Apple ID password. I typed it wrong the first time. I got it correct the second time, and the update process seemed to continue for half a second, but then suddenly AppStore crashed (and I filled out and sent the error report thingy).

On restarting AppStore/checking for updates, now I only see the Evernote update available.

Should I leave things as they are? Or should I manually try to update Java and iTunes? Are TimeMachine backups helpful in this situation?

I really don't want any inconsistent state/corrupt files/unstable system/etc.

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    Restart your computer and try it again. This is the beauty of TM backups - if you nuke your machine, it's fine. Just restart and try again. – Undo Mar 5 '13 at 22:12
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You can go to Apple.com and download any Apple Updates manually: http://support.apple.com/downloads/

And there's no harm in "reapplying" them. In fact, sometimes it's a good troubleshooting measure.

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