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In recent editions of Canon's Digital Photo Professional (beyond version 3.11.10 or later) a lens correction tool known as Digital Lens Optimizer (DLO) has been added. It uses Canon's own knowledge of the complete design and performance of Canon sensors and lenses to apply comprehensive lens correction to RAW files. Applying DLO correction to a .cr2 file doubles the size of the RAW file. If the DLO correction for that file is later unchecked in DPP, the file size reverts back to the original.

What could cause this?

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According to Canon,

Digital Photo Professional writes additional information for the DLO processing to the RAW image; the result is that the RAW image file will increase in size, often significantly.

It saves not only the new corrected image in RAW format but also the original image into the file - or at least the steps taken to get from the original to the corrected version. The issue is that the Cr2 file has to be still readable by other RAW format capable software to read the corrected image, but still preserve the old image for a reversal of the process.

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    \$\begingroup\$ Other RAW convertors do not read the corrected image. They display the original file. To get LR to use the corrected image it must be exported from DPP as a TIFF that is even larger than the double sized RAW file. \$\endgroup\$
    – Michael C
    Commented Mar 1, 2013 at 18:17

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