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I do not know what has gone wrong with my D: drive. The drive is absolutely fine, data is present.

I can unmount/mount the drive; but cannot view files and folders in it. When I try to ls the drive from the terminal I get the following error:

ls: cannot access found.001: Input/output error

This was working fine till 2 days back, but it seems I have deleted some file. Can someone please help figure out how can I view them again?

Wubi is installed in the E: drive.

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You need to run chkdsk from Windows. There appears to be some filesystem corruption and since it's NTFS you have to run it from Windows.

Boot Windows, open My Computer, right click on D:, Properties, Tools, Check disk for errors. That should clear it up.

Note that the \found.??? directories are system protected and hidden by default and are used to recover corrupted files/directories.

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