When using Canon's raw format CR2, there is no modification of the data by the capturing software. So Backyard EOS does not change the data in any form.
However, there is an old issue with the Batch FormatConversion script (also see
https://pixinsight.com/forum/index.php?topic=12228.15 , reply #15) that will prevent the Debayer tool from working with the Bayer/mosaic pattern set to 'Auto':
BatchFormatConversion does not write properties to the file. This means, that the information about the Bayer/mosaic pattern is missing in the converted file. Debayer then generates the error message: "*** Error: Unable to acquire CFA pattern information: Required image metadata not available.".
I reported this issue to Juan on 3rd January 2020 and he replied that he will fix this issue as soon as possible.
Bernd