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You can use Winclone to make a back up of your Windows partition onto the Mac OS X side and then it will be backed up using Time Machine, so if you restore from your Time Machine back up you can then restore your windows partition using Bootcamp Assistant and Winclone. (You'll have to make the Bootcamp partition the same size as the previous one unless you're using NTFS which can be expanded to any size as long as it's the same size or larger)
 
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