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After upgrading the BIOS, I was no longer able to SSH into the box. I consoled in via IPMI and saw "Checking the filesystem" messages. I had the data center team take a look; they told me the filesystem is corrupt.

Can someone help me understand how BIOS changes can affect the disk/filesystem?

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    The cause is not necessarily the BIOS upgrade itself, the fact that you need to reboot / powercycle the system to effect such an upgrade might be the actual reason that the file-system corruption appeared. – HBruijn Jan 18 at 7:33
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A bad BIOS update can in principle break your system in just about any way. But a broken file system is a highly unlikely outcome of that. The most likely outcome of a bad BIOS upgrade is that the system either doesn't boot or it boots but doesn't detect all hardware. Neither would manifest itself as an error during file system check.

A much more likely scenario is that your file system had some latent corruption that was bound to show up on the next reboot regardless of the reason for the reboot.

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BIOS update can't corrupt/change filesystem. But bad shutdown process can. FOr example powering off the machine instead of doing graceful shutdown put filesystem(s) in inconsistent state. Also during this poweroff all write operations in the OS make the filesystem inconsistent.

What you can do is to try to repair your filesystem(s) during boot process (via IPMI console)

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