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restore acronis backup on empty partition of hdd with installed operating system

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If I restore acronis backup (os and programs) on empty partition of hdd with installed operating system, one of operating systems will become unbootable. How to do both operating systems bootable?

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You can boot on the Windows installation DVD, get to a command prompt, then use the bootrec command to "/scanOS" for bootable OS, "/rebuildBCD"
http://support.microsoft.com/kb/927392#method1

You can also use third party bootloaders to set up your system easily.