I use Adobe Lightroom and even they do not write the metadate insede original RAW files (like NEF or CR2). They write metadata insede DNG files (a universal RAW format file format made by Adobe).
You can convert your files into DNG and use Lightroom and you will have only one file.
Maybe Canon Software knows how to write data into CR2.
But I do not think that Adobe or others will modify NEF or CR2 files.