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The title pretty much sums up the question.

I'm using windows 8.1 and ubuntu 12.04 in dualboot and now something in windows 8.1 broke and by the looks of it I may have to refresh/reinstall it.

Since I had to go through hell installing ubuntu (removing uefi boot, manually installing ubuntu then launching boot repair which created boot-grub for both ubuntu and windows) I can't figure out what will happen if I let windows 8.1 refresh/reinstall itself (windows 8.1 comes with a button for that and I may have to use it).

There are numerous questions about installing ubuntu alongside windows 8.1 but how to safely remove one or the other without having to throw your HDD?

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If you reinstall windows it will make ubuntu not bootable. Ubuntu will still be there unless you repartition your drive, it just will not be accessible:

There is a section in this wiki that deals with installing windows after ubuntu. https://help.ubuntu.com/community/WindowsDualBoot

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Many OEM Windows recovery tools will reset the entire disk to factory state. In other words, they'll wipe out Linux. A Windows retail disc is less likely to do this, at least if you're careful with your options. –  Rod Smith Mar 15 at 14:39
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