I have my laptop split between Windows Vista and Ubuntu Linux. I recently upgraded Ubuntu and it somehow fraked up my Windows and now it will not load. I need to fix Windows so I can get back to my iTunes but I don't want to do anything that will mess up my Ubuntu either. Any suggestions?

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Have you created a "Restore point" in windows ?
If so than you can easily store to that point

you may find that the boot (grub) if you are duel booting has been damaged. It may be a linux forum question but if it boots ubuntu and not windows then it is likely you need to modify grub. regretably I can only suggest a reinstall of ubuntu but other in linux will know better.
M

Back up your data to other PC pull out your HDD and make a back up before you proceed i suggest reinstall your OS,,

If you have created recovery disk. Run that recovery disk, might it will solve your problem.

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