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I don’t use Windows but I believe you have to set the PC to show hidden files before you can see the System folder.
As for the extensions.cfg file, perhaps the best starting point is to open up the extensions.cfg file in the Koreader files you have downloaded (use something like Notepad or Notepad++). You will see that against each file type there is reader app name - where there is more than one reader app name (they are separated by a comma) the first name is the default. Against ePub you will see Koreader.app has been set as the reader app.
If you look at the extensions.cfg in the download of Cool Reader, you will see something like cr3-pb.app set as the default reader for epub.
To give you the option to choose between reader apps, just amend the relevant file type line of code for example:
epub:@EPUB_file:1:cr3-pb.app,eink-reader.app,koreader.app:ICON_EPUB
...this gives the option to open ePub with Cool Reader, the in-built reader app or Koreader but Cool Reader is set as the default because it comes first.
The extensions.cfg file sits in System/config on the Pocketbook.
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