Why corrupt .CR2 file from 350D (NOT Lightroom caused).

The XT/350D is an older model that uses CF cards. Due to the wear-leveling technology that's built into CF, checking the card for write errors isn't super-useful. The blocks that are written to one time are different from the blocks that are written to the next time. The higher-level checks like FAT and directory consistency are still useful — but if you routinely format your card to erase the files, you shouldn't ever run into those problems.

Given the low cost of memory cards these days, it's usually cheaper and safer to simply discard any memory card you don't fully trust and replace it with a new one.

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The open-source LightZone Project: http://lightzoneproject.org/