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I have an external hdd which is formatted with fat for use by both on linux and windows. The issue is that I can't delete some of the files I have which show up with size 0. Also, the modification timestamp (as detected by Krusader, the file manager I am using) is 1935. How can I delete these kind of files without affecting the running fs?

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It would help to know why you can't delete them - without the error message it'll be hard to help you. – Cry Havok Oct 11 '10 at 20:04
I agree with @CryHavok, otherwise use "rm -f" – Lightly Salted Oct 11 '10 at 20:09
Doh, sorry, here's the error: rm: cannot remove `file': Input/output error – hyperboreean Oct 11 '10 at 20:18
Have you run fsck or equivalent on the file system? – Cry Havok Oct 11 '10 at 21:48
“Input/output error” points to a damaged filesystem or a damaged disk. Do any messages show up in /var/log/kern.log (better check from the time you plug in the disk to the time you get the error)? – Gilles Oct 11 '10 at 22:40

Most likely your FAT table is damaged. You can run fsck to see if this is indeed the case. But I would recommend finding other tools (ie. Testdisk) to fix FAT table before you run fsck to "fix" it...if you value the other data on the drive.

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