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At the moment I have a 1.5tb WD HDD with Ubuntu 14.04 loaded on it. Instead of booting up Ubuntu I want to boot windows off of a sandisk 240gb SSD I also have installed. Every time I look at the drive in files while in Ubuntu it says that the disk contains an unclean file system. Please help as soon as possible.

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The unclean file system message has a very simple explanation - your Windows is not shut down but hibernated. You should start Windows, disable hibernation (run "powercfg -h off" command in an elevated command prompt), shutdown Windows, start Linux and I'm 99.99% confident you'll not get the unclean file system message anymore.

It's not clear from your post what you mean by "I want to boot windows" part - are you trying to boot Windows and fail? Just remove the Linux HDD and let only the Windows HDD in the system and try like this. Anyway, if you moved the Windows HDD from another system it might fail booting (and even if it will boot it will most probably miss drivers and/or ask to re-activate due to the hardware changes).

You should boot the Windows HDD on the system where Windows was installed. After you disable hibernation as instructed above and shut down than you could move the HDD to the Linux system in order to access files from it (but not booting Windows from it) from Linux.

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