Windows 8 won't boot after deleting files in C drive from Ubuntu

I have done a very stupid thing. I deleted some folders in the C: drive from Ubuntu. In result, I can't boot into Windows anymore. It starts the boot animation and then keeps rebooting.

I tried checkdisk, sfc/scannow and the automatic repair but it doesn't work. What is strange is that I can boot into safe mode so I think my Windows installation is intact. Also checkdisk and sfc say no errors found. From Ubuntu, I only delete Windows.old folder.

Any suggestions? Is there anyway I can see the exact error. May be a log file or something. I tried EventViewer, and System32/Logs but everything seems normal.

Maybe I could try /fixmbr and /fixboot commands. If I do so do I have to reinstall GRUB afterwords?

Just because Windows can limp its way into safe mode doesn't mean it's "intact", just that it's not completely hosed. Your MBR, boot sector and file system structures are probably fine, but you've deleted some files that Windows needs during a normal (not safe mode) startup.

To fix the problem, I'd recommend refreshing your Windows 8 installation. This should restore the missing files from your Windows installation disc or recovery volume, allowing you to boot normally into Windows again.

(Ps. Just deleting the Windows.old folder shouldn't have broken your system, if that's indeed all you did. However, I suppose it's possible that deleting it from Linux might've removed something like user settings that were still in use, and which Windows would've been smart enough to save elsewhere first if you'd deleted the folder from inside Windows.)

During a fresh install of windows all the data is deleted and new drivers and softwares are installed. But if any hardware you got with which you got a Driver CD you need to install it again on a fresh install.

This doesn't happen with installing windows on a previous installation and then deleting the Windows.old folder. In this case when you install a windows on a previously installed windows, old windows have the drivers for the current hardware, new windows will always load up from the windows.old folder till you provide a new installation in the current windows (i.e. new windows). And if you deleted that folder(windows.old) without installing the drivers again you would probably have similar problems as you are having. So always try to install drivers for external hardware(hardware having their own drivers CD) before deleting windows.old folder on this type of installation.